AutoCloner

Multiple sequence alignment - TraesCS2B01G456800

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	TraesCS2B01G456800	chr2B	100.000	3104	0	0	1	3104	651724304	651727407	0.000000e+00	5733
1	TraesCS2B01G456800	chr2B	100.000	890	0	0	1	890	199167100	199166211	0.000000e+00	1644
2	TraesCS2B01G456800	chr2B	100.000	890	0	0	1	890	528830402	528831291	0.000000e+00	1644
3	TraesCS2B01G456800	chr2A	91.393	2254	124	31	891	3104	688425770	688423547	0.000000e+00	3024
4	TraesCS2B01G456800	chr2A	100.000	890	0	0	1	890	55883930	55883041	0.000000e+00	1644
5	TraesCS2B01G456800	chr2A	100.000	890	0	0	1	890	771618382	771617493	0.000000e+00	1644
6	TraesCS2B01G456800	chr2D	90.062	2244	137	34	891	3074	545003191	545005408	0.000000e+00	2830
7	TraesCS2B01G456800	chr2D	91.272	1203	91	7	891	2082	462481055	462479856	0.000000e+00	1628
8	TraesCS2B01G456800	chr3B	90.447	1476	111	16	891	2341	242194899	242193429	0.000000e+00	1917
9	TraesCS2B01G456800	chr3D	90.408	1470	119	14	891	2341	166492698	166491232	0.000000e+00	1914
10	TraesCS2B01G456800	chr3D	99.888	890	1	0	1	890	3362993	3363882	0.000000e+00	1639
11	TraesCS2B01G456800	chr3A	91.067	1321	98	8	983	2287	204867513	204866197	0.000000e+00	1768
12	TraesCS2B01G456800	chr6B	100.000	890	0	0	1	890	717855734	717854845	0.000000e+00	1644
13	TraesCS2B01G456800	chr5B	100.000	890	0	0	1	890	63282174	63281285	0.000000e+00	1644
14	TraesCS2B01G456800	chr5B	100.000	890	0	0	1	890	362955662	362954773	0.000000e+00	1644
15	TraesCS2B01G456800	chr6D	99.888	890	1	0	1	890	432917568	432916679	0.000000e+00	1639
16	TraesCS2B01G456800	chr4A	90.579	605	46	5	1326	1920	554085173	554084570	0.000000e+00	791
17	TraesCS2B01G456800	chr4D	91.743	327	15	6	1326	1641	45311550	45311875	7.900000e-121	444

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	TraesCS2B01G456800	chr2B	651724304	651727407	3103	False	5733	5733	100.000	1	3104	1	chr2B.!!$F2	3103
1	TraesCS2B01G456800	chr2B	199166211	199167100	889	True	1644	1644	100.000	1	890	1	chr2B.!!$R1	889
2	TraesCS2B01G456800	chr2B	528830402	528831291	889	False	1644	1644	100.000	1	890	1	chr2B.!!$F1	889
3	TraesCS2B01G456800	chr2A	688423547	688425770	2223	True	3024	3024	91.393	891	3104	1	chr2A.!!$R2	2213
4	TraesCS2B01G456800	chr2A	55883041	55883930	889	True	1644	1644	100.000	1	890	1	chr2A.!!$R1	889
5	TraesCS2B01G456800	chr2A	771617493	771618382	889	True	1644	1644	100.000	1	890	1	chr2A.!!$R3	889
6	TraesCS2B01G456800	chr2D	545003191	545005408	2217	False	2830	2830	90.062	891	3074	1	chr2D.!!$F1	2183
7	TraesCS2B01G456800	chr2D	462479856	462481055	1199	True	1628	1628	91.272	891	2082	1	chr2D.!!$R1	1191
8	TraesCS2B01G456800	chr3B	242193429	242194899	1470	True	1917	1917	90.447	891	2341	1	chr3B.!!$R1	1450
9	TraesCS2B01G456800	chr3D	166491232	166492698	1466	True	1914	1914	90.408	891	2341	1	chr3D.!!$R1	1450
10	TraesCS2B01G456800	chr3D	3362993	3363882	889	False	1639	1639	99.888	1	890	1	chr3D.!!$F1	889
11	TraesCS2B01G456800	chr3A	204866197	204867513	1316	True	1768	1768	91.067	983	2287	1	chr3A.!!$R1	1304
12	TraesCS2B01G456800	chr6B	717854845	717855734	889	True	1644	1644	100.000	1	890	1	chr6B.!!$R1	889
13	TraesCS2B01G456800	chr5B	63281285	63282174	889	True	1644	1644	100.000	1	890	1	chr5B.!!$R1	889
14	TraesCS2B01G456800	chr5B	362954773	362955662	889	True	1644	1644	100.000	1	890	1	chr5B.!!$R2	889
15	TraesCS2B01G456800	chr6D	432916679	432917568	889	True	1639	1639	99.888	1	890	1	chr6D.!!$R1	889
16	TraesCS2B01G456800	chr4A	554084570	554085173	603	True	791	791	90.579	1326	1920	1	chr4A.!!$R1	594

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
1010	1012	1.467374	GCATTACGCCATGTGTTCACC	60.467	52.381	0.37	0.0	32.94	4.02	F
1983	2006	0.260230	CCCTCCAGCTGACTCTCCTA	59.740	60.000	17.39	0.0	0.00	2.94	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2082	2105	0.112995	ATGTGAGCCCTTGAAAGCCA	59.887	50.0	0.0	0.0	0.0	4.75	R
2794	2881	0.736325	CTGGGCGAACTGAAGGTACG	60.736	60.0	0.0	0.0	0.0	3.67	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
1010	1012	1.467374	GCATTACGCCATGTGTTCACC	60.467	52.381	0.37	0.00	32.94	4.02
1026	1028	5.800438	GTGTTCACCAAACTCTTGTCTTTTC	59.200	40.000	0.00	0.00	38.76	2.29
1104	1117	3.639094	GAGTTCTAGAGGCAGCTATGGAA	59.361	47.826	0.00	0.00	0.00	3.53
1195	1208	7.769044	TCTTATACAAGGGCAATAAAGACTGTC	59.231	37.037	0.00	0.00	32.22	3.51
1270	1283	5.065235	TCAGTGATTCTTCATTGACTGCAA	58.935	37.500	0.00	0.00	41.91	4.08
1295	1308	3.402628	ACAAACGTTAGCTGACCTGAT	57.597	42.857	0.00	0.00	0.00	2.90
1306	1319	5.021033	AGCTGACCTGATAACAATCTCTG	57.979	43.478	0.00	0.00	0.00	3.35
1459	1476	3.412386	ACAGTATCCCAGTGCTTTGAAC	58.588	45.455	0.00	0.00	0.00	3.18
1521	1538	2.977405	AGCTTTGTTTTGCTCTAGCG	57.023	45.000	0.00	0.00	45.83	4.26
1650	1671	0.607489	CAACCTTGGACCTCTGCAGG	60.607	60.000	15.13	1.31	46.87	4.85
1779	1800	8.520351	CAACAATCTTGCATCATGGATATATGT	58.480	33.333	0.00	0.00	0.00	2.29
1816	1839	6.015350	CAGTATGGGTATATTTCTCGAGGTGT	60.015	42.308	13.56	1.05	0.00	4.16
1819	1842	6.795144	TGGGTATATTTCTCGAGGTGTTTA	57.205	37.500	13.56	0.00	0.00	2.01
1912	1935	3.136123	CCACGATGGGCTTGCTGG	61.136	66.667	0.00	0.00	32.67	4.85
1979	2002	0.324275	GTCTCCCTCCAGCTGACTCT	60.324	60.000	17.39	0.00	0.00	3.24
1983	2006	0.260230	CCCTCCAGCTGACTCTCCTA	59.740	60.000	17.39	0.00	0.00	2.94
1990	2013	4.661240	TCCAGCTGACTCTCCTACTATACT	59.339	45.833	17.39	0.00	0.00	2.12
2043	2066	4.518211	GCCCAAGGAATGATACTCTCAATG	59.482	45.833	0.00	0.00	37.44	2.82
2063	2086	2.045634	GGTGCCAGCTCTGATGCA	60.046	61.111	0.00	0.00	34.99	3.96
2082	2105	2.928731	GCAAGTAGAAGCGCTTGTCTCT	60.929	50.000	30.47	20.79	42.76	3.10
2237	2263	5.363868	CACAAGTGATCTCAATAGGAGGGTA	59.636	44.000	0.00	0.00	44.19	3.69
2280	2311	2.871022	CAAGTGTATGAGCAGAGCCATC	59.129	50.000	0.00	0.00	0.00	3.51
2308	2342	1.620739	ATGAGAGGCACGGTGCTGAT	61.621	55.000	29.92	17.57	44.28	2.90
2309	2343	1.078848	GAGAGGCACGGTGCTGATT	60.079	57.895	29.92	14.83	44.28	2.57
2343	2377	4.828296	GGCATGGGAGTGCTGGGG	62.828	72.222	0.00	0.00	44.45	4.96
2344	2378	3.731728	GCATGGGAGTGCTGGGGA	61.732	66.667	0.00	0.00	41.82	4.81
2352	2386	1.821136	GGAGTGCTGGGGATTTCAAAG	59.179	52.381	0.00	0.00	0.00	2.77
2368	2402	7.067981	GGATTTCAAAGGTGATATTCTGAGCTT	59.932	37.037	0.00	0.00	32.48	3.74
2412	2446	1.248785	CCTCGTCCTTCCACTCCGAA	61.249	60.000	0.00	0.00	0.00	4.30
2474	2521	6.528537	TGTATTTTGGTGCTTATTCTGCAT	57.471	33.333	0.00	0.00	42.69	3.96
2483	2530	1.538512	CTTATTCTGCATCCATGGCCG	59.461	52.381	6.96	0.72	0.00	6.13
2517	2564	0.596083	TTCAATGCAACGCCGTTTGG	60.596	50.000	0.00	0.00	38.77	3.28
2566	2621	0.389948	AGTCGTCCCGTGCAAGATTC	60.390	55.000	0.00	0.00	0.00	2.52
2581	2636	1.347707	AGATTCTGTTCCAACGGCAGA	59.652	47.619	0.00	0.00	37.47	4.26
2621	2680	8.166422	ACGGAATTTTTAACTGACAGAAGATT	57.834	30.769	10.08	0.35	0.00	2.40
2633	2692	5.125356	TGACAGAAGATTGCAGTCTGAAAA	58.875	37.500	13.02	0.00	41.08	2.29
2642	2701	4.979943	TGCAGTCTGAAAAACATGTCAA	57.020	36.364	3.32	0.00	0.00	3.18
2645	2704	4.734402	GCAGTCTGAAAAACATGTCAAGCA	60.734	41.667	3.32	0.00	0.00	3.91
2646	2705	4.736793	CAGTCTGAAAAACATGTCAAGCAC	59.263	41.667	0.00	0.00	0.00	4.40
2647	2706	4.641989	AGTCTGAAAAACATGTCAAGCACT	59.358	37.500	0.00	0.00	0.00	4.40
2648	2707	4.972440	GTCTGAAAAACATGTCAAGCACTC	59.028	41.667	0.00	0.00	0.00	3.51
2649	2708	4.639755	TCTGAAAAACATGTCAAGCACTCA	59.360	37.500	0.00	0.00	0.00	3.41
2650	2709	5.300034	TCTGAAAAACATGTCAAGCACTCAT	59.700	36.000	0.00	0.00	0.00	2.90
2651	2710	5.283294	TGAAAAACATGTCAAGCACTCATG	58.717	37.500	0.00	0.00	42.86	3.07
2664	2723	2.219458	CACTCATGCTAATGCCTCAGG	58.781	52.381	0.00	0.00	38.71	3.86
2724	2808	1.985116	GAGGAGGCACCGGAGAAGT	60.985	63.158	9.46	0.00	44.74	3.01
2757	2844	3.988976	TCCAGTGATTTCTCTTGGAGG	57.011	47.619	0.00	0.00	33.63	4.30
2794	2881	1.339151	GGTGGATGACTGAACCAGACC	60.339	57.143	0.45	0.00	35.18	3.85
2808	2895	1.402456	CCAGACCGTACCTTCAGTTCG	60.402	57.143	0.00	0.00	38.83	3.95
2849	2951	7.670344	CTATCTATAGATGGTGCGCAGGAGC	62.670	52.000	23.03	2.23	38.61	4.70
2854	2956	2.437359	GGTGCGCAGGAGCTCAAT	60.437	61.111	12.22	0.00	44.77	2.57
2864	2966	5.401550	CGCAGGAGCTCAATTTTCAAATTA	58.598	37.500	17.19	0.00	36.33	1.40
2871	2973	8.671028	GGAGCTCAATTTTCAAATTAATGCAAT	58.329	29.630	17.19	0.00	36.52	3.56
2964	3066	7.549147	TTAGTTTGGAGAGTAGTACACCAAT	57.451	36.000	19.58	12.53	39.75	3.16
3023	3125	3.954904	TGATCTTGTAGTACCAGCTCCTC	59.045	47.826	0.00	0.00	0.00	3.71
3037	3139	3.015327	AGCTCCTCAAATTGTGCTCATC	58.985	45.455	0.00	0.00	0.00	2.92
3039	3141	3.181499	GCTCCTCAAATTGTGCTCATCAG	60.181	47.826	0.00	0.00	0.00	2.90
3040	3142	4.259356	CTCCTCAAATTGTGCTCATCAGA	58.741	43.478	0.00	0.00	0.00	3.27
3050	3152	3.380954	TGTGCTCATCAGAAAAGTTGCAA	59.619	39.130	0.00	0.00	0.00	4.08
3074	3176	3.318839	TCATCCAAACAACAGCTTCCAAG	59.681	43.478	0.00	0.00	0.00	3.61
3075	3177	2.733956	TCCAAACAACAGCTTCCAAGT	58.266	42.857	0.00	0.00	0.00	3.16
3076	3178	3.096092	TCCAAACAACAGCTTCCAAGTT	58.904	40.909	0.00	0.00	0.00	2.66
3077	3179	3.130340	TCCAAACAACAGCTTCCAAGTTC	59.870	43.478	0.00	0.00	0.00	3.01
3078	3180	3.447742	CAAACAACAGCTTCCAAGTTCC	58.552	45.455	0.00	0.00	0.00	3.62

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1010	1012	5.818136	TGACCAGAAAAGACAAGAGTTTG	57.182	39.130	0.00	0.00	40.24	2.93
1026	1028	7.469181	GCCTGGAAATACAATAAAGATGACCAG	60.469	40.741	0.00	0.00	39.43	4.00
1104	1117	7.392673	TGTTCCGTAAGTATAACAGAAGACTCT	59.607	37.037	0.00	0.00	31.65	3.24
1140	1153	2.159282	GCTCGGAAGGAATCGACTTGTA	60.159	50.000	0.00	0.00	0.00	2.41
1195	1208	5.591472	TCTTCAAACATAGGAATCTGGCATG	59.409	40.000	0.00	0.00	0.00	4.06
1306	1319	6.542735	GGGTACAGAGGGAGAAAATATTTGTC	59.457	42.308	0.39	2.13	0.00	3.18
1459	1476	6.128634	GCATTTGAAAGATCTCCAAGCAAAAG	60.129	38.462	0.00	1.91	0.00	2.27
1521	1538	0.901124	AGTCCATGTCAGGAGCAGAC	59.099	55.000	0.00	0.00	38.64	3.51
1641	1662	4.133078	GGATAATGAAAGACCTGCAGAGG	58.867	47.826	17.39	2.02	46.21	3.69
1650	1671	3.059597	CGATGCCACGGATAATGAAAGAC	60.060	47.826	0.00	0.00	0.00	3.01
1651	1672	3.130633	CGATGCCACGGATAATGAAAGA	58.869	45.455	0.00	0.00	0.00	2.52
1779	1800	1.613317	CCATACTGCCACCGAGGTCA	61.613	60.000	0.00	0.00	40.61	4.02
1816	1839	9.113838	GCTTATCTGTGGATCTGAATTTCTAAA	57.886	33.333	0.00	0.00	33.71	1.85
1819	1842	5.757320	CGCTTATCTGTGGATCTGAATTTCT	59.243	40.000	0.00	0.00	33.71	2.52
1912	1935	3.729163	GCGCTCAGTTTAGGAAGATTTGC	60.729	47.826	0.00	0.00	0.00	3.68
1979	2002	5.893500	AGAATGCTAGGCAGTATAGTAGGA	58.106	41.667	0.00	0.00	43.65	2.94
1983	2006	5.510520	GCAAGAGAATGCTAGGCAGTATAGT	60.511	44.000	0.00	0.00	43.65	2.12
1990	2013	1.407851	CCTGCAAGAGAATGCTAGGCA	60.408	52.381	0.67	0.00	46.54	4.75
2043	2066	1.812922	CATCAGAGCTGGCACCGAC	60.813	63.158	0.00	0.00	0.00	4.79
2063	2086	2.353208	CCAGAGACAAGCGCTTCTACTT	60.353	50.000	22.21	4.17	0.00	2.24
2082	2105	0.112995	ATGTGAGCCCTTGAAAGCCA	59.887	50.000	0.00	0.00	0.00	4.75
2237	2263	1.750778	CGCCAGAAATACCAAGCCAAT	59.249	47.619	0.00	0.00	0.00	3.16
2308	2342	3.485394	TGCCAGACAGTAGCAATTGAAA	58.515	40.909	10.34	0.00	32.56	2.69
2309	2343	3.138884	TGCCAGACAGTAGCAATTGAA	57.861	42.857	10.34	0.00	32.56	2.69
2343	2377	7.565323	AGCTCAGAATATCACCTTTGAAATC	57.435	36.000	0.00	0.00	34.61	2.17
2344	2378	7.613022	TCAAGCTCAGAATATCACCTTTGAAAT	59.387	33.333	0.00	0.00	34.61	2.17
2368	2402	6.701145	AGATAACGAGAATAACTGAGCTCA	57.299	37.500	17.19	17.19	0.00	4.26
2379	2413	4.716794	AGGACGAGGTAGATAACGAGAAT	58.283	43.478	0.00	0.00	0.00	2.40
2381	2415	3.834489	AGGACGAGGTAGATAACGAGA	57.166	47.619	0.00	0.00	0.00	4.04
2412	2446	2.076863	GTACGCTGCCAGTTGAGAATT	58.923	47.619	0.00	0.00	0.00	2.17
2474	2521	2.927856	ACAGGTGTCGGCCATGGA	60.928	61.111	18.40	0.00	0.00	3.41
2483	2530	3.829948	CATTGAATTCTGCACAGGTGTC	58.170	45.455	7.05	0.00	0.00	3.67
2522	2569	1.690219	CCCGTCTGAGCCAGGCTAAT	61.690	60.000	16.16	0.00	39.88	1.73
2566	2621	0.886490	AAGCTCTGCCGTTGGAACAG	60.886	55.000	0.00	0.00	42.39	3.16
2581	2636	1.073199	CCGTTGGGTTCAGGAAGCT	59.927	57.895	10.63	0.00	38.72	3.74
2621	2680	4.734402	GCTTGACATGTTTTTCAGACTGCA	60.734	41.667	0.00	0.00	0.00	4.41
2645	2704	2.634815	CCTGAGGCATTAGCATGAGT	57.365	50.000	0.00	0.00	44.61	3.41
2658	2717	2.612115	AGAACTGGGGGCCTGAGG	60.612	66.667	0.84	0.00	0.00	3.86
2659	2718	1.920325	TGAGAACTGGGGGCCTGAG	60.920	63.158	0.84	1.68	0.00	3.35
2660	2719	2.206900	TGAGAACTGGGGGCCTGA	59.793	61.111	0.84	0.00	0.00	3.86
2661	2720	2.352805	GTGAGAACTGGGGGCCTG	59.647	66.667	0.84	0.00	0.00	4.85
2662	2721	2.936032	GGTGAGAACTGGGGGCCT	60.936	66.667	0.84	0.00	0.00	5.19
2663	2722	2.936032	AGGTGAGAACTGGGGGCC	60.936	66.667	0.00	0.00	0.00	5.80
2664	2723	2.671682	GAGGTGAGAACTGGGGGC	59.328	66.667	0.00	0.00	0.00	5.80
2665	2724	2.660064	CGGAGGTGAGAACTGGGGG	61.660	68.421	0.00	0.00	0.00	5.40
2794	2881	0.736325	CTGGGCGAACTGAAGGTACG	60.736	60.000	0.00	0.00	0.00	3.67
2808	2895	0.972983	TAGACAGTGAGAGGCTGGGC	60.973	60.000	0.00	0.00	38.22	5.36
2864	2966	7.231925	TGCTTATCTGTGAATGGATATTGCATT	59.768	33.333	0.00	0.00	41.19	3.56
2871	2973	6.737720	ACTCTGCTTATCTGTGAATGGATA	57.262	37.500	0.00	0.00	0.00	2.59
2873	2975	5.658634	AGTACTCTGCTTATCTGTGAATGGA	59.341	40.000	0.00	0.00	0.00	3.41
2878	2980	5.068329	CCATCAGTACTCTGCTTATCTGTGA	59.932	44.000	0.00	0.00	41.10	3.58
3023	3125	6.563381	GCAACTTTTCTGATGAGCACAATTTG	60.563	38.462	0.00	0.00	0.00	2.32
3037	3139	4.572985	TGGATGAGTTGCAACTTTTCTG	57.427	40.909	31.58	0.00	39.88	3.02
3039	3141	5.108517	TGTTTGGATGAGTTGCAACTTTTC	58.891	37.500	31.58	27.09	39.88	2.29
3040	3142	5.083533	TGTTTGGATGAGTTGCAACTTTT	57.916	34.783	31.58	21.74	39.88	2.27
3050	3152	2.887152	GGAAGCTGTTGTTTGGATGAGT	59.113	45.455	0.00	0.00	0.00	3.41
3074	3176	1.886542	GATTGGTGGTCAGGTTGGAAC	59.113	52.381	0.00	0.00	0.00	3.62
3075	3177	1.496857	TGATTGGTGGTCAGGTTGGAA	59.503	47.619	0.00	0.00	0.00	3.53
3076	3178	1.144691	TGATTGGTGGTCAGGTTGGA	58.855	50.000	0.00	0.00	0.00	3.53
3077	3179	1.613437	GTTGATTGGTGGTCAGGTTGG	59.387	52.381	0.00	0.00	0.00	3.77
3078	3180	1.613437	GGTTGATTGGTGGTCAGGTTG	59.387	52.381	0.00	0.00	0.00	3.77

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.