AutoCloner

Multiple sequence alignment - TraesCS3A01G066100

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	TraesCS3A01G066100	chr3A	100.000	3155	0	0	1	3155	39184479	39187633	0.000000e+00	5827
1	TraesCS3A01G066100	chr3A	92.835	3182	158	28	1	3155	38691498	38694636	0.000000e+00	4549
2	TraesCS3A01G066100	chr3A	92.889	2672	166	20	489	3155	39858182	39860834	0.000000e+00	3860
3	TraesCS3A01G066100	chr3A	93.240	2633	154	21	536	3155	39307131	39309752	0.000000e+00	3855
4	TraesCS3A01G066100	chr3A	93.202	2633	155	21	536	3155	39323863	39326484	0.000000e+00	3849
5	TraesCS3A01G066100	chr3A	94.127	2503	127	13	654	3155	39573909	39576392	0.000000e+00	3790
6	TraesCS3A01G066100	chr3A	92.473	2604	159	24	576	3155	39658251	39660841	0.000000e+00	3688
7	TraesCS3A01G066100	chr3A	92.293	2608	159	13	576	3155	39677910	39680503	0.000000e+00	3664
8	TraesCS3A01G066100	chr3A	92.862	1541	88	11	856	2388	39698446	39699972	0.000000e+00	2217
9	TraesCS3A01G066100	chr3A	93.226	310	21	0	576	885	39698136	39698445	1.030000e-124	457
10	TraesCS3A01G066100	chr3A	94.662	281	15	0	576	856	39443037	39443317	1.340000e-118	436
11	TraesCS3A01G066100	chr3A	96.241	133	3	2	489	619	39573776	39573908	1.910000e-52	217
12	TraesCS3A01G066100	chr3A	88.276	145	14	3	160	303	55843175	55843033	1.500000e-38	171
13	TraesCS3A01G066100	chr3D	87.151	1541	164	15	1586	3097	29371739	29373274	0.000000e+00	1718
14	TraesCS3A01G066100	chr3D	88.577	534	35	11	308	839	29285007	29285516	2.670000e-175	625
15	TraesCS3A01G066100	chr3D	88.800	500	48	5	960	1453	29361755	29362252	9.680000e-170	606
16	TraesCS3A01G066100	chr3D	90.032	311	29	2	308	616	29361279	29361589	4.900000e-108	401
17	TraesCS3A01G066100	chr3D	89.655	145	14	1	5	148	9269783	9269639	1.930000e-42	183
18	TraesCS3A01G066100	chr3D	89.247	93	10	0	1448	1540	29371642	29371734	1.990000e-22	117
19	TraesCS3A01G066100	chr3B	86.421	1193	145	10	1942	3122	50061612	50062799	0.000000e+00	1290
20	TraesCS3A01G066100	chr3B	91.549	284	20	4	335	616	50061164	50061445	3.820000e-104	388
21	TraesCS3A01G066100	chr3B	88.816	152	17	0	160	311	828175768	828175617	1.490000e-43	187
22	TraesCS3A01G066100	chr3B	89.655	145	14	1	5	148	62105674	62105530	1.930000e-42	183
23	TraesCS3A01G066100	chr1B	90.789	152	14	0	154	305	543763000	543762849	1.480000e-48	204
24	TraesCS3A01G066100	chr1B	88.961	154	17	0	152	305	35178808	35178961	1.160000e-44	191
25	TraesCS3A01G066100	chr1B	90.441	136	13	0	151	286	668290398	668290263	2.500000e-41	180
26	TraesCS3A01G066100	chr6B	92.029	138	8	3	5	140	7429950	7429814	1.160000e-44	191
27	TraesCS3A01G066100	chr4B	88.387	155	18	0	151	305	667253940	667253786	1.490000e-43	187
28	TraesCS3A01G066100	chr1D	90.141	142	13	1	8	148	4767196	4767055	1.930000e-42	183
29	TraesCS3A01G066100	chr1D	88.356	146	15	2	4	148	13748147	13748003	1.160000e-39	174
30	TraesCS3A01G066100	chrUn	87.662	154	19	0	152	305	16380754	16380907	2.500000e-41	180
31	TraesCS3A01G066100	chrUn	87.671	146	15	2	5	148	332687288	332687144	1.950000e-37	167
32	TraesCS3A01G066100	chr7B	90.370	135	10	3	5	137	7028656	7028523	1.160000e-39	174
33	TraesCS3A01G066100	chr7B	86.928	153	19	1	153	305	513723283	513723434	1.500000e-38	171
34	TraesCS3A01G066100	chr2D	88.276	145	16	1	5	148	534646015	534646159	4.180000e-39	172
35	TraesCS3A01G066100	chr2D	86.452	155	21	0	151	305	94866537	94866691	1.500000e-38	171

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	TraesCS3A01G066100	chr3A	39184479	39187633	3154	False	5827.0	5827	100.000	1	3155	1	chr3A.!!$F2	3154
1	TraesCS3A01G066100	chr3A	38691498	38694636	3138	False	4549.0	4549	92.835	1	3155	1	chr3A.!!$F1	3154
2	TraesCS3A01G066100	chr3A	39858182	39860834	2652	False	3860.0	3860	92.889	489	3155	1	chr3A.!!$F8	2666
3	TraesCS3A01G066100	chr3A	39307131	39309752	2621	False	3855.0	3855	93.240	536	3155	1	chr3A.!!$F3	2619
4	TraesCS3A01G066100	chr3A	39323863	39326484	2621	False	3849.0	3849	93.202	536	3155	1	chr3A.!!$F4	2619
5	TraesCS3A01G066100	chr3A	39658251	39660841	2590	False	3688.0	3688	92.473	576	3155	1	chr3A.!!$F6	2579
6	TraesCS3A01G066100	chr3A	39677910	39680503	2593	False	3664.0	3664	92.293	576	3155	1	chr3A.!!$F7	2579
7	TraesCS3A01G066100	chr3A	39573776	39576392	2616	False	2003.5	3790	95.184	489	3155	2	chr3A.!!$F9	2666
8	TraesCS3A01G066100	chr3A	39698136	39699972	1836	False	1337.0	2217	93.044	576	2388	2	chr3A.!!$F10	1812
9	TraesCS3A01G066100	chr3D	29371642	29373274	1632	False	917.5	1718	88.199	1448	3097	2	chr3D.!!$F3	1649
10	TraesCS3A01G066100	chr3D	29285007	29285516	509	False	625.0	625	88.577	308	839	1	chr3D.!!$F1	531
11	TraesCS3A01G066100	chr3D	29361279	29362252	973	False	503.5	606	89.416	308	1453	2	chr3D.!!$F2	1145
12	TraesCS3A01G066100	chr3B	50061164	50062799	1635	False	839.0	1290	88.985	335	3122	2	chr3B.!!$F1	2787

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
76	77	0.037790	GAGCAGGTCATATCTCCGGC	60.038	60.0	0.00	8.91	43.26	6.13	F
177	194	0.107017	CCGGCCATGTGGAAGAGATT	60.107	55.0	2.24	0.00	37.39	2.40	F
1415	1573	0.102300	GCAAGAAGTTTTGCGGTGGT	59.898	50.0	6.91	0.00	43.36	4.16	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1309	1467	0.035725	CTCATCTGCCTGCAAGTCCA	60.036	55.000	0.00	0.00	0.00	4.02	R
2115	2298	2.505819	AGGACTTCTGATAATGCCCGTT	59.494	45.455	0.00	0.00	0.00	4.44	R
2455	2649	0.030101	AATTGTTCGGTTGCACCACG	59.970	50.000	6.21	2.35	38.47	4.94	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
36	37	2.606725	CGCATAAGAGCACTTCAAGAGG	59.393	50.000	0.00	0.00	37.53	3.69
41	42	6.294176	GCATAAGAGCACTTCAAGAGGAAAAA	60.294	38.462	0.00	0.00	37.53	1.94
44	45	4.453819	AGAGCACTTCAAGAGGAAAAATCG	59.546	41.667	0.00	0.00	34.44	3.34
47	48	3.821033	CACTTCAAGAGGAAAAATCGGGT	59.179	43.478	0.00	0.00	34.44	5.28
73	74	2.765122	GCTTGAGCAGGTCATATCTCC	58.235	52.381	2.40	0.00	41.59	3.71
74	75	2.865670	GCTTGAGCAGGTCATATCTCCG	60.866	54.545	2.40	0.00	41.59	4.63
76	77	0.037790	GAGCAGGTCATATCTCCGGC	60.038	60.000	0.00	8.91	43.26	6.13
77	78	0.760567	AGCAGGTCATATCTCCGGCA	60.761	55.000	15.99	0.00	44.82	5.69
135	137	7.230849	TGATCTGCAAATTGTAGGACAAATT	57.769	32.000	11.01	0.00	41.96	1.82
177	194	0.107017	CCGGCCATGTGGAAGAGATT	60.107	55.000	2.24	0.00	37.39	2.40
185	202	3.887621	TGTGGAAGAGATTTAGTCCCG	57.112	47.619	0.00	0.00	0.00	5.14
209	226	4.313819	GGCCAACCGGGACTAAAG	57.686	61.111	6.32	0.00	43.78	1.85
210	227	1.378119	GGCCAACCGGGACTAAAGG	60.378	63.158	6.32	0.00	43.78	3.11
211	228	1.378119	GCCAACCGGGACTAAAGGG	60.378	63.158	6.32	0.00	40.01	3.95
212	229	2.072366	CCAACCGGGACTAAAGGGT	58.928	57.895	6.32	0.00	40.01	4.34
213	230	0.322187	CCAACCGGGACTAAAGGGTG	60.322	60.000	6.32	0.00	42.16	4.61
214	231	0.322187	CAACCGGGACTAAAGGGTGG	60.322	60.000	6.32	0.00	38.99	4.61
242	259	4.773013	TGTAGTCCCGATTTATTTGTCCC	58.227	43.478	0.00	0.00	0.00	4.46
248	265	3.011119	CCGATTTATTTGTCCCGGTTGA	58.989	45.455	0.00	0.00	33.02	3.18
418	435	9.758651	GGAAATTTAGTTTTACACACTTGGAAT	57.241	29.630	0.00	0.00	0.00	3.01
625	645	7.549488	AGTTAAATCGCAAAAGCATCTACTACT	59.451	33.333	0.00	0.00	0.00	2.57
665	719	1.454847	GCCGGGCCATTGGTGATTA	60.455	57.895	8.12	0.00	0.00	1.75
851	906	6.028987	TCGATTGACATGAATTCGTTACGTA	58.971	36.000	4.24	0.00	0.00	3.57
856	911	6.327154	TGACATGAATTCGTTACGTAGTCAT	58.673	36.000	18.33	18.33	41.01	3.06
917	1042	8.124199	CGATTGACATTGATCACAATCACAATA	58.876	33.333	24.85	5.99	44.71	1.90
1103	1259	2.612221	GCCCTCTTGTACTGTACACCAC	60.612	54.545	19.57	3.98	38.63	4.16
1191	1347	1.435168	ACCCTTCTTCTCTCCTCCTGT	59.565	52.381	0.00	0.00	0.00	4.00
1415	1573	0.102300	GCAAGAAGTTTTGCGGTGGT	59.898	50.000	6.91	0.00	43.36	4.16
1494	1652	4.508124	GTCCTGTCATTCAAGTATAAGCGG	59.492	45.833	0.00	0.00	0.00	5.52
1603	1761	4.583871	ACCCAGACTCATCAAGATGTTTC	58.416	43.478	9.66	7.50	39.72	2.78
1677	1842	8.997621	TTTGTTTATCCTGTGTGTATCTCTAC	57.002	34.615	0.00	0.00	0.00	2.59
1683	1848	5.008331	TCCTGTGTGTATCTCTACTTCGTT	58.992	41.667	0.00	0.00	0.00	3.85
1694	1859	7.589958	ATCTCTACTTCGTTTATGTGGAGAT	57.410	36.000	12.99	12.99	46.49	2.75
1749	1915	7.164803	TGGTTGATTTGTTTTTGAAAAGGAGT	58.835	30.769	0.00	0.00	0.00	3.85
1758	1924	8.541899	TGTTTTTGAAAAGGAGTATTAACCCT	57.458	30.769	0.00	0.00	0.00	4.34
1776	1942	2.492012	CCTCAGCATCTACATCAAGCC	58.508	52.381	0.00	0.00	0.00	4.35
1991	2171	3.589735	TGTCTTGTTCCCATTTAGCCCTA	59.410	43.478	0.00	0.00	0.00	3.53
2109	2292	6.653526	TTCTCATGACAAATGTTCCATGTT	57.346	33.333	12.31	0.00	38.00	2.71
2115	2298	6.951062	TGACAAATGTTCCATGTTGAACTA	57.049	33.333	13.72	3.99	43.96	2.24
2117	2300	7.199766	TGACAAATGTTCCATGTTGAACTAAC	58.800	34.615	13.72	0.00	43.96	2.34
2212	2396	3.751518	AGCATTACCGAAAGTCCTTGTT	58.248	40.909	0.00	0.00	0.00	2.83
2226	2410	7.559590	AAGTCCTTGTTAGCATTATCATGAC	57.440	36.000	0.00	0.00	31.07	3.06
2228	2412	5.822519	GTCCTTGTTAGCATTATCATGACCA	59.177	40.000	0.00	0.00	31.07	4.02
2304	2497	5.576447	ATTCCATCCCGTTTTCATTACAC	57.424	39.130	0.00	0.00	0.00	2.90
2318	2511	6.403866	TTCATTACACCATGAGCTTTTTGT	57.596	33.333	0.00	0.00	34.59	2.83
2455	2649	7.259290	TCAGGAAATATTATGCGTCTTTTCC	57.741	36.000	11.20	11.20	41.42	3.13
2456	2650	6.018262	TCAGGAAATATTATGCGTCTTTTCCG	60.018	38.462	12.46	9.52	44.25	4.30
2590	2784	7.395772	TGAAATATTGTGTCCAAATTAGGCTCA	59.604	33.333	0.00	0.00	33.44	4.26
2665	2859	9.243637	TGTTATGAAAATTTTGCAAGTACTCAC	57.756	29.630	8.47	0.00	0.00	3.51
2740	2934	1.334054	GCATTGCGACTCAAAAGCTG	58.666	50.000	0.00	0.00	38.34	4.24
2788	2982	3.121328	CGATTCGACTATTCATTGCCGAC	60.121	47.826	0.00	0.00	0.00	4.79
2869	3067	4.594920	CCACATACTACTCCCTCCATTCAT	59.405	45.833	0.00	0.00	0.00	2.57
3001	3199	9.515226	TTGCATTTTTGAATAGAAGTAGTACCT	57.485	29.630	0.00	0.00	0.00	3.08
3034	3232	5.297776	ACAAAATCTCCTCGCTATTCCATTG	59.702	40.000	0.00	0.00	0.00	2.82
3060	3258	3.343941	TTATTCCACGGTTGCTAGCTT	57.656	42.857	17.23	0.00	0.00	3.74
3061	3259	2.200373	ATTCCACGGTTGCTAGCTTT	57.800	45.000	17.23	0.00	0.00	3.51

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
53	54	2.765122	GGAGATATGACCTGCTCAAGC	58.235	52.381	0.00	0.00	42.50	4.01
73	74	3.131396	GGTGTAATGGTATTCTCTGCCG	58.869	50.000	0.00	0.00	30.91	5.69
74	75	4.423625	AGGTGTAATGGTATTCTCTGCC	57.576	45.455	0.00	0.00	0.00	4.85
76	77	6.428159	GGCATTAGGTGTAATGGTATTCTCTG	59.572	42.308	7.14	0.00	44.06	3.35
77	78	6.330250	AGGCATTAGGTGTAATGGTATTCTCT	59.670	38.462	7.14	0.00	44.06	3.10
135	137	2.559668	AGCGCGCCCTTTAGTATATACA	59.440	45.455	30.33	0.00	0.00	2.29
165	182	2.500098	CCGGGACTAAATCTCTTCCACA	59.500	50.000	0.00	0.00	0.00	4.17
177	194	3.384532	GCCACGACCCGGGACTAA	61.385	66.667	32.02	0.00	28.17	2.24
199	216	1.905512	CTCCCACCCTTTAGTCCCG	59.094	63.158	0.00	0.00	0.00	5.14
203	220	0.475828	ACAGGCTCCCACCCTTTAGT	60.476	55.000	0.00	0.00	0.00	2.24
204	221	1.486726	CTACAGGCTCCCACCCTTTAG	59.513	57.143	0.00	0.00	0.00	1.85
206	223	0.475828	ACTACAGGCTCCCACCCTTT	60.476	55.000	0.00	0.00	0.00	3.11
208	225	1.306226	GACTACAGGCTCCCACCCT	60.306	63.158	0.00	0.00	0.00	4.34
209	226	2.368011	GGACTACAGGCTCCCACCC	61.368	68.421	0.00	0.00	0.00	4.61
210	227	2.368011	GGGACTACAGGCTCCCACC	61.368	68.421	3.98	0.00	45.22	4.61
211	228	2.722201	CGGGACTACAGGCTCCCAC	61.722	68.421	9.22	0.00	46.11	4.61
212	229	2.238319	ATCGGGACTACAGGCTCCCA	62.238	60.000	9.22	0.00	46.11	4.37
213	230	1.049289	AATCGGGACTACAGGCTCCC	61.049	60.000	0.00	0.00	42.73	4.30
214	231	0.831307	AAATCGGGACTACAGGCTCC	59.169	55.000	0.00	0.00	0.00	4.70
221	238	3.805971	CGGGACAAATAAATCGGGACTAC	59.194	47.826	0.00	0.00	0.00	2.73
248	265	1.632965	GGCCTTTAGTCCCGGGTCAT	61.633	60.000	22.86	10.32	0.00	3.06
273	290	4.886579	GGAACAACCTTTAGTCTCGGTTA	58.113	43.478	0.00	0.00	38.90	2.85
418	435	8.845413	AAAATGTTCATGCCTGCTAAAAATTA	57.155	26.923	0.00	0.00	0.00	1.40
455	472	7.883217	TCTACGGGTTTAAAAATAAATGTGCA	58.117	30.769	0.00	0.00	0.00	4.57
625	645	1.409064	CGACTAGCATGGCAGTAAGGA	59.591	52.381	0.00	0.00	0.00	3.36
746	800	9.930693	ACAAGAGATTTTATCTAGAAGAACGTT	57.069	29.630	0.00	0.00	40.38	3.99
936	1061	9.950680	GAATTCACGTAATGGATTAATTGTGAT	57.049	29.630	0.00	0.79	36.56	3.06
937	1062	8.951243	TGAATTCACGTAATGGATTAATTGTGA	58.049	29.630	3.38	0.00	36.56	3.58
938	1063	9.734620	ATGAATTCACGTAATGGATTAATTGTG	57.265	29.630	11.07	0.00	36.56	3.33
1103	1259	1.424493	GCTCTTCTTCACCATCGCCG	61.424	60.000	0.00	0.00	0.00	6.46
1191	1347	1.144708	TCAACCTCTTTGTGGGCATCA	59.855	47.619	0.00	0.00	36.49	3.07
1309	1467	0.035725	CTCATCTGCCTGCAAGTCCA	60.036	55.000	0.00	0.00	0.00	4.02
1581	1739	4.288105	AGAAACATCTTGATGAGTCTGGGT	59.712	41.667	16.43	0.00	0.00	4.51
1677	1842	5.748630	TCAATCGATCTCCACATAAACGAAG	59.251	40.000	0.00	0.00	32.48	3.79
1749	1915	6.994421	TGATGTAGATGCTGAGGGTTAATA	57.006	37.500	0.00	0.00	0.00	0.98
1758	1924	3.473625	CATGGCTTGATGTAGATGCTGA	58.526	45.455	0.00	0.00	0.00	4.26
1776	1942	9.585099	ACTATTTAATAAATGGTTGTGTGCATG	57.415	29.630	8.63	0.00	39.19	4.06
1920	2097	4.761235	AGAAAGACTTGCATCATGTGTG	57.239	40.909	0.00	0.00	0.00	3.82
2109	2292	4.746535	TCTGATAATGCCCGTTAGTTCA	57.253	40.909	0.00	0.00	0.00	3.18
2115	2298	2.505819	AGGACTTCTGATAATGCCCGTT	59.494	45.455	0.00	0.00	0.00	4.44
2117	2300	2.874701	CAAGGACTTCTGATAATGCCCG	59.125	50.000	0.00	0.00	0.00	6.13
2304	2497	6.015940	AGGAGAAAACTACAAAAAGCTCATGG	60.016	38.462	0.00	0.00	0.00	3.66
2318	2511	6.870971	AACAATTTGCGTAGGAGAAAACTA	57.129	33.333	0.00	0.00	0.00	2.24
2354	2547	9.861138	TGAAGAACGATTGCAAAAATAAATTTG	57.139	25.926	1.71	0.00	42.01	2.32
2455	2649	0.030101	AATTGTTCGGTTGCACCACG	59.970	50.000	6.21	2.35	38.47	4.94
2456	2650	1.857837	CAAATTGTTCGGTTGCACCAC	59.142	47.619	6.21	0.00	38.47	4.16
2590	2784	3.434309	CCTTGAAGAATGGATGGTGGTT	58.566	45.455	0.00	0.00	0.00	3.67
2740	2934	3.763897	AGGTATTGTTGCCAAACATCCTC	59.236	43.478	0.00	0.00	45.54	3.71
2761	2955	6.021390	CGGCAATGAATAGTCGAATCGTATAG	60.021	42.308	1.52	0.00	0.00	1.31
2763	2957	4.621460	CGGCAATGAATAGTCGAATCGTAT	59.379	41.667	1.52	0.00	0.00	3.06
3001	3199	9.832445	ATAGCGAGGAGATTTTGTATTCTAAAA	57.168	29.630	0.00	0.00	0.00	1.52
3034	3232	2.353579	AGCAACCGTGGAATAAATACGC	59.646	45.455	0.00	0.00	36.56	4.42
3041	3239	3.343941	AAAGCTAGCAACCGTGGAATA	57.656	42.857	18.83	0.00	0.00	1.75
3060	3258	3.203487	AGAAGTTTGGTGGGTGAGGTTAA	59.797	43.478	0.00	0.00	0.00	2.01
3061	3259	2.781174	AGAAGTTTGGTGGGTGAGGTTA	59.219	45.455	0.00	0.00	0.00	2.85

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.