AutoCloner

Multiple sequence alignment - TraesCS4B01G196200

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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	TraesCS4B01G196200	chr4B	100.000	3778	0	0	1	3778	423036027	423039804	0.000000e+00	6977
1	TraesCS4B01G196200	chr4B	86.042	960	89	13	1	916	13381703	13382661	0.000000e+00	989
2	TraesCS4B01G196200	chr4B	86.304	920	86	10	41	922	69303315	69302398	0.000000e+00	965
3	TraesCS4B01G196200	chr4B	81.974	466	60	13	475	918	110822332	110822795	1.280000e-99	374
4	TraesCS4B01G196200	chr4A	95.348	1999	50	9	914	2886	125469851	125467870	0.000000e+00	3136
5	TraesCS4B01G196200	chr4A	92.593	351	17	2	2886	3227	125467814	125467464	2.620000e-136	496
6	TraesCS4B01G196200	chr4A	90.610	213	13	1	3291	3503	125467465	125467260	3.720000e-70	276
7	TraesCS4B01G196200	chr4A	91.358	81	6	1	3657	3736	125466872	125466792	3.990000e-20	110
8	TraesCS4B01G196200	chr2A	95.317	1986	52	11	920	2888	657131042	657129081	0.000000e+00	3114
9	TraesCS4B01G196200	chr2A	91.379	812	31	5	3005	3778	657128854	657128044	0.000000e+00	1075
10	TraesCS4B01G196200	chr2A	96.269	134	4	1	2883	3015	657129031	657128898	6.350000e-53	219
11	TraesCS4B01G196200	chr4D	95.513	1939	51	10	962	2888	341388834	341390748	0.000000e+00	3066
12	TraesCS4B01G196200	chr4D	93.784	917	33	6	2883	3778	341392782	341393695	0.000000e+00	1356
13	TraesCS4B01G196200	chr2D	87.802	951	81	12	3	918	92868216	92867266	0.000000e+00	1081
14	TraesCS4B01G196200	chr6B	87.421	946	84	16	3	922	35540476	35541412	0.000000e+00	1055
15	TraesCS4B01G196200	chr6B	87.421	946	84	16	3	922	35554240	35555176	0.000000e+00	1055
16	TraesCS4B01G196200	chr6D	87.716	928	77	14	3	893	439488645	439489572	0.000000e+00	1048
17	TraesCS4B01G196200	chr6D	81.010	911	146	24	24	922	409482155	409483050	0.000000e+00	699
18	TraesCS4B01G196200	chr3D	86.097	971	77	21	3	922	567547250	567548213	0.000000e+00	992
19	TraesCS4B01G196200	chr7B	86.403	934	85	13	3	899	495186362	495185434	0.000000e+00	983
20	TraesCS4B01G196200	chr1B	85.759	955	99	17	1	918	468502332	468501378	0.000000e+00	976
21	TraesCS4B01G196200	chr5B	84.942	943	113	15	3	918	548220146	548221086	0.000000e+00	928
22	TraesCS4B01G196200	chr3B	84.304	962	102	18	3	918	732872700	732873658	0.000000e+00	894
23	TraesCS4B01G196200	chr3B	84.625	826	91	20	9	810	480427981	480428794	0.000000e+00	789
24	TraesCS4B01G196200	chr5D	86.000	100	10	4	1155	1253	410562479	410562575	1.860000e-18	104

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	TraesCS4B01G196200	chr4B	423036027	423039804	3777	False	6977.000000	6977	100.000000	1	3778	1	chr4B.!!$F3	3777
1	TraesCS4B01G196200	chr4B	13381703	13382661	958	False	989.000000	989	86.042000	1	916	1	chr4B.!!$F1	915
2	TraesCS4B01G196200	chr4B	69302398	69303315	917	True	965.000000	965	86.304000	41	922	1	chr4B.!!$R1	881
3	TraesCS4B01G196200	chr4A	125466792	125469851	3059	True	1004.500000	3136	92.477250	914	3736	4	chr4A.!!$R1	2822
4	TraesCS4B01G196200	chr2A	657128044	657131042	2998	True	1469.333333	3114	94.321667	920	3778	3	chr2A.!!$R1	2858
5	TraesCS4B01G196200	chr4D	341388834	341393695	4861	False	2211.000000	3066	94.648500	962	3778	2	chr4D.!!$F1	2816
6	TraesCS4B01G196200	chr2D	92867266	92868216	950	True	1081.000000	1081	87.802000	3	918	1	chr2D.!!$R1	915
7	TraesCS4B01G196200	chr6B	35540476	35541412	936	False	1055.000000	1055	87.421000	3	922	1	chr6B.!!$F1	919
8	TraesCS4B01G196200	chr6B	35554240	35555176	936	False	1055.000000	1055	87.421000	3	922	1	chr6B.!!$F2	919
9	TraesCS4B01G196200	chr6D	439488645	439489572	927	False	1048.000000	1048	87.716000	3	893	1	chr6D.!!$F2	890
10	TraesCS4B01G196200	chr6D	409482155	409483050	895	False	699.000000	699	81.010000	24	922	1	chr6D.!!$F1	898
11	TraesCS4B01G196200	chr3D	567547250	567548213	963	False	992.000000	992	86.097000	3	922	1	chr3D.!!$F1	919
12	TraesCS4B01G196200	chr7B	495185434	495186362	928	True	983.000000	983	86.403000	3	899	1	chr7B.!!$R1	896
13	TraesCS4B01G196200	chr1B	468501378	468502332	954	True	976.000000	976	85.759000	1	918	1	chr1B.!!$R1	917
14	TraesCS4B01G196200	chr5B	548220146	548221086	940	False	928.000000	928	84.942000	3	918	1	chr5B.!!$F1	915
15	TraesCS4B01G196200	chr3B	732872700	732873658	958	False	894.000000	894	84.304000	3	918	1	chr3B.!!$F2	915
16	TraesCS4B01G196200	chr3B	480427981	480428794	813	False	789.000000	789	84.625000	9	810	1	chr3B.!!$F1	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
888	1027	0.250381	ACGATTTTACCGTGTGGGCA	60.250	50.0	0.0	0.0	40.62	5.36	F
1039	1178	0.391263	GCTTCTCCTTGTACCCCACG	60.391	60.0	0.0	0.0	0.00	4.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2631	2798	3.738282	GCTTACATCCTCAATCAGTAGCG	59.262	47.826	0.0	0.0	0.00	4.26	R
3015	5222	0.035152	TGCTGGCTTGTCCTATGGTG	60.035	55.000	0.0	0.0	35.26	4.17	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
58	59	8.731605	CCAAAGCATAGATAGATAGAACTACGA	58.268	37.037	0.00	0.00	0.00	3.43
64	65	9.715123	CATAGATAGATAGAACTACGATGCAAG	57.285	37.037	0.00	0.00	0.00	4.01
134	173	0.762418	TCATCCTCGGTGGTGTTGTT	59.238	50.000	0.00	0.00	37.07	2.83
171	210	0.612744	TGTCATCCCAACGCAGATCA	59.387	50.000	0.00	0.00	0.00	2.92
218	257	5.806366	TCGTTCTCGACAATATCACACTA	57.194	39.130	0.00	0.00	41.35	2.74
428	468	2.087646	CTGGTCAGTGATGAGACGAGA	58.912	52.381	0.00	0.00	41.36	4.04
595	637	2.893895	CGTCGGACCGGATCTCGA	60.894	66.667	15.25	8.83	42.43	4.04
607	649	2.645802	GGATCTCGACAGAGTACCAGT	58.354	52.381	0.00	0.00	44.65	4.00
657	715	1.974875	GGAAAAACCCCGGCGACAT	60.975	57.895	9.30	0.00	0.00	3.06
688	767	1.362406	GGAAAGCGGCGAGAAAGAGG	61.362	60.000	12.98	0.00	0.00	3.69
717	796	4.070552	GAGGAGAAGGGCGCGTGT	62.071	66.667	8.43	0.00	0.00	4.49
751	830	1.153647	CGTGGCGAGTGCTGGATTA	60.154	57.895	0.00	0.00	42.25	1.75
754	833	2.135933	GTGGCGAGTGCTGGATTATAC	58.864	52.381	0.00	0.00	42.25	1.47
806	885	3.368571	GCCAGCTGCCGCTTTCTT	61.369	61.111	8.66	0.00	46.47	2.52
816	952	2.358247	GCTTTCTTCCCCGCACGA	60.358	61.111	0.00	0.00	0.00	4.35
848	986	2.100631	CCGTTGGAGCTCGCGAAAT	61.101	57.895	20.39	0.16	0.00	2.17
888	1027	0.250381	ACGATTTTACCGTGTGGGCA	60.250	50.000	0.00	0.00	40.62	5.36
899	1038	1.077357	TGTGGGCACGTCTTTTGGT	60.077	52.632	0.00	0.00	0.00	3.67
905	1044	3.284449	ACGTCTTTTGGTGCGCCC	61.284	61.111	15.15	6.44	0.00	6.13
935	1074	8.613482	GGAGATGCTTTTATAGGTGTAAGTTTC	58.387	37.037	0.00	0.00	0.00	2.78
950	1089	3.347077	AGTTTCCTCCATGCAGAAGAG	57.653	47.619	0.00	0.00	0.00	2.85
1039	1178	0.391263	GCTTCTCCTTGTACCCCACG	60.391	60.000	0.00	0.00	0.00	4.94
1162	1324	6.406692	TCGAAGAAGAGAGGAAAAAGAGAA	57.593	37.500	0.00	0.00	0.00	2.87
1719	1881	5.403466	GCGATGGGCTTTTGATTATTGATTC	59.597	40.000	0.00	0.00	39.11	2.52
1741	1903	5.683681	TCATGCACTTCTAGCCAATGATTA	58.316	37.500	0.00	0.00	0.00	1.75
1801	1963	2.364970	CAGGATTTGCAAAACACTGGGA	59.635	45.455	17.19	0.00	0.00	4.37
1802	1964	3.007182	CAGGATTTGCAAAACACTGGGAT	59.993	43.478	17.19	0.00	0.00	3.85
1803	1965	4.220382	CAGGATTTGCAAAACACTGGGATA	59.780	41.667	17.19	0.00	0.00	2.59
1804	1966	4.463891	AGGATTTGCAAAACACTGGGATAG	59.536	41.667	17.19	0.00	0.00	2.08
1805	1967	4.462483	GGATTTGCAAAACACTGGGATAGA	59.538	41.667	17.19	0.00	0.00	1.98
1806	1968	5.393461	GGATTTGCAAAACACTGGGATAGAG	60.393	44.000	17.19	0.00	0.00	2.43
1807	1969	4.365514	TTGCAAAACACTGGGATAGAGA	57.634	40.909	0.00	0.00	0.00	3.10
1808	1970	4.365514	TGCAAAACACTGGGATAGAGAA	57.634	40.909	0.00	0.00	0.00	2.87
1809	1971	4.326826	TGCAAAACACTGGGATAGAGAAG	58.673	43.478	0.00	0.00	0.00	2.85
1810	1972	4.041567	TGCAAAACACTGGGATAGAGAAGA	59.958	41.667	0.00	0.00	0.00	2.87
1811	1973	4.393371	GCAAAACACTGGGATAGAGAAGAC	59.607	45.833	0.00	0.00	0.00	3.01
1942	2104	2.164219	GCGCTTTCATTCCTTTGATCCA	59.836	45.455	0.00	0.00	0.00	3.41
1961	2127	4.086457	TCCAAAGGGCATAGGAAAAGTTC	58.914	43.478	0.00	0.00	0.00	3.01
2003	2169	7.068702	AGGGATTATTCACATAGGAATTTGCA	58.931	34.615	0.00	0.00	38.41	4.08
2007	2173	9.188588	GATTATTCACATAGGAATTTGCATGTG	57.811	33.333	18.38	18.38	46.16	3.21
2028	2194	6.541086	TGTGTGTTTGCATTTGAATTTCAAC	58.459	32.000	11.30	1.80	35.89	3.18
2034	2200	6.601741	TTGCATTTGAATTTCAACTGGTTC	57.398	33.333	23.07	12.23	37.47	3.62
2035	2201	4.744137	TGCATTTGAATTTCAACTGGTTCG	59.256	37.500	23.07	5.82	37.47	3.95
2109	2275	9.646427	TGAAAACACAAAAATTACAGCTAAAGT	57.354	25.926	0.00	0.00	0.00	2.66
2631	2798	0.884514	GGGCAGCAAGGAAGAAAGTC	59.115	55.000	0.00	0.00	0.00	3.01
2764	2931	6.758416	TGCTCTTACATGAAGTATAAGCTGTG	59.242	38.462	0.00	0.00	39.49	3.66
2845	3012	9.499479	AAGTCAGATGCATATCATTTTACCTAG	57.501	33.333	0.00	0.00	35.05	3.02
2958	5165	1.143401	GGGACCTACTTGCGCCTAC	59.857	63.158	4.18	0.00	0.00	3.18
3120	5390	4.599047	AGCTCTCCATGTAGCAGATTAC	57.401	45.455	12.73	0.00	41.32	1.89
3122	5392	4.406972	AGCTCTCCATGTAGCAGATTACAA	59.593	41.667	12.73	0.00	41.32	2.41
3151	5421	8.671384	TGTGCCCATCTATATACAACTAAAAC	57.329	34.615	0.00	0.00	0.00	2.43
3188	5458	8.607459	GCGGGATATAATCATTGAACAGATAAG	58.393	37.037	0.00	0.00	0.00	1.73
3298	5586	5.173673	GCACATCACAAATACACAACACAAG	59.826	40.000	0.00	0.00	0.00	3.16
3299	5587	6.264832	CACATCACAAATACACAACACAAGT	58.735	36.000	0.00	0.00	0.00	3.16
3513	5801	1.555075	ACCGAGGCAGATAGCTCAAAA	59.445	47.619	0.00	0.00	44.79	2.44
3553	5841	2.278330	GGGGTTTGCCTGCCTGAAG	61.278	63.158	0.00	0.00	34.45	3.02
3611	5900	4.681978	GCAAGGTCGGCGTCCAGT	62.682	66.667	24.24	9.55	0.00	4.00
3655	6177	2.282958	ACGAAGGAGCTCCGACCA	60.283	61.111	26.95	0.00	42.08	4.02
3665	6187	2.363795	TCCGACCAAGGCGAGGAT	60.364	61.111	5.26	0.00	0.00	3.24
3672	6194	1.094073	CCAAGGCGAGGATGAGCTTG	61.094	60.000	0.00	0.00	0.00	4.01

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
171	210	1.765314	CAGTCGATCTTCTCCCCCAAT	59.235	52.381	0.00	0.00	0.00	3.16
207	246	5.304614	ACTGGCCTTATCGTAGTGTGATATT	59.695	40.000	3.32	0.00	0.00	1.28
213	252	1.134788	GCACTGGCCTTATCGTAGTGT	60.135	52.381	16.05	0.00	40.52	3.55
277	316	2.928002	CCTTCTGGGCAGAGAGGAT	58.072	57.895	0.00	0.00	38.88	3.24
386	426	2.358247	GTGCGGACCATGTTCGGT	60.358	61.111	0.00	0.00	43.91	4.69
595	637	0.966920	CCCAACGACTGGTACTCTGT	59.033	55.000	7.39	0.00	44.76	3.41
639	681	1.974875	ATGTCGCCGGGGTTTTTCC	60.975	57.895	19.13	1.78	0.00	3.13
643	685	3.961414	ACCATGTCGCCGGGGTTT	61.961	61.111	19.13	1.55	0.00	3.27
717	796	2.661537	CGCGCTCAACCACACTGA	60.662	61.111	5.56	0.00	0.00	3.41
742	821	0.599991	CGCGCCTGTATAATCCAGCA	60.600	55.000	0.00	0.00	0.00	4.41
751	830	2.885644	CTTCACGCGCGCCTGTAT	60.886	61.111	32.58	6.00	0.00	2.29
806	885	1.448893	GCAAACTATCGTGCGGGGA	60.449	57.895	0.00	0.00	0.00	4.81
813	930	1.743995	GGTGGCGGCAAACTATCGT	60.744	57.895	15.50	0.00	0.00	3.73
816	952	1.302993	AACGGTGGCGGCAAACTAT	60.303	52.632	15.50	0.00	0.00	2.12
881	1020	1.077357	ACCAAAAGACGTGCCCACA	60.077	52.632	0.00	0.00	0.00	4.17
888	1027	3.284449	GGGCGCACCAAAAGACGT	61.284	61.111	10.83	0.00	39.85	4.34
905	1044	4.876107	ACACCTATAAAAGCATCTCCAACG	59.124	41.667	0.00	0.00	0.00	4.10
935	1074	3.197333	TCTCTTTCTCTTCTGCATGGAGG	59.803	47.826	14.84	0.00	0.00	4.30
950	1089	3.366781	GCCATTTTCAGCAGGTCTCTTTC	60.367	47.826	0.00	0.00	0.00	2.62
1191	1353	0.764752	CCATCTCCTGGTACTCCCCC	60.765	65.000	0.00	0.00	40.49	5.40
1585	1747	1.680522	GCGAGAGGCCATGAGAAGGA	61.681	60.000	5.01	0.00	34.80	3.36
1703	1865	9.582431	AGAAGTGCATGAATCAATAATCAAAAG	57.418	29.630	0.00	0.00	0.00	2.27
1719	1881	4.913335	AATCATTGGCTAGAAGTGCATG	57.087	40.909	0.00	0.00	0.00	4.06
1942	2104	3.763057	ACGAACTTTTCCTATGCCCTTT	58.237	40.909	0.00	0.00	0.00	3.11
1961	2127	8.792830	ATAATCCCTATGATTTCAACCATACG	57.207	34.615	0.00	0.00	40.92	3.06
2003	2169	6.922247	TGAAATTCAAATGCAAACACACAT	57.078	29.167	0.00	0.00	0.00	3.21
2028	2194	5.565592	TTCAATTGATGGATTCGAACCAG	57.434	39.130	19.48	9.13	40.89	4.00
2035	2201	4.980434	CCGAATGCTTCAATTGATGGATTC	59.020	41.667	34.52	34.52	45.12	2.52
2109	2275	4.225942	CCTATTGAGGCCATAAGGATAGCA	59.774	45.833	5.01	0.00	35.54	3.49
2335	2501	6.884280	AAACCAAACAATGTTCCAAACAAA	57.116	29.167	0.00	0.00	45.86	2.83
2370	2536	4.966366	GCAGTCATGACATTTCGCTTATTC	59.034	41.667	27.02	0.00	0.00	1.75
2631	2798	3.738282	GCTTACATCCTCAATCAGTAGCG	59.262	47.826	0.00	0.00	0.00	4.26
2661	2828	8.031277	GTGCCAGATGATCAAAAAGTTAAGATT	58.969	33.333	0.00	0.00	0.00	2.40
2764	2931	7.709947	TCTGAAGCACATTTTAATGGATGATC	58.290	34.615	7.33	0.00	40.70	2.92
2888	3055	8.939201	TTTTTGAACTTTGCAGATAATGTGAA	57.061	26.923	0.00	0.00	0.00	3.18
2935	5142	1.173913	GCGCAAGTAGGTCCCAAAAT	58.826	50.000	0.30	0.00	41.68	1.82
3015	5222	0.035152	TGCTGGCTTGTCCTATGGTG	60.035	55.000	0.00	0.00	35.26	4.17
3016	5223	0.254178	CTGCTGGCTTGTCCTATGGT	59.746	55.000	0.00	0.00	35.26	3.55
3018	5225	0.543277	TCCTGCTGGCTTGTCCTATG	59.457	55.000	4.42	0.00	35.26	2.23
3019	5226	0.543749	GTCCTGCTGGCTTGTCCTAT	59.456	55.000	4.42	0.00	35.26	2.57
3120	5390	5.559770	TGTATATAGATGGGCACATGGTTG	58.440	41.667	5.94	0.00	37.47	3.77
3122	5392	5.310594	AGTTGTATATAGATGGGCACATGGT	59.689	40.000	5.94	0.00	37.47	3.55
3151	5421	5.872617	TGATTATATCCCGCTCCAATTTACG	59.127	40.000	0.00	0.00	0.00	3.18
3188	5458	5.238868	TGAGAGCGATATACTGACAAGGTAC	59.761	44.000	0.00	0.00	0.00	3.34
3260	5530	2.609002	TGATGTGCTTGTGCTATTAGCG	59.391	45.455	10.94	0.00	46.26	4.26
3394	5682	3.070878	TCTGTTGTTGGTCATGCTCTGTA	59.929	43.478	0.00	0.00	0.00	2.74
3409	5697	1.072159	GTGCTGCTCCCTCTGTTGT	59.928	57.895	0.00	0.00	0.00	3.32
3553	5841	1.134175	CCTCCTCGTGCTCTTCTTCTC	59.866	57.143	0.00	0.00	0.00	2.87
3594	5883	3.291101	TACTGGACGCCGACCTTGC	62.291	63.158	7.20	0.00	0.00	4.01
3630	5919	4.484258	GCTCCTTCGTCTCGCGCT	62.484	66.667	5.56	0.00	41.07	5.92
3647	5936	2.427245	ATCCTCGCCTTGGTCGGAG	61.427	63.158	4.32	2.09	0.00	4.63
3655	6177	0.177604	CTCAAGCTCATCCTCGCCTT	59.822	55.000	0.00	0.00	0.00	4.35
3665	6187	1.219124	GCCACGGATCTCAAGCTCA	59.781	57.895	0.00	0.00	0.00	4.26

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.