AutoCloner

Multiple sequence alignment - TraesCS2B01G068300

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	TraesCS2B01G068300	chr2B	100.000	2690	0	0	1	2690	34865452	34862763	0.000000e+00	4968.0
1	TraesCS2B01G068300	chr2B	88.338	1955	190	22	451	2386	34890326	34888391	0.000000e+00	2313.0
2	TraesCS2B01G068300	chr2B	91.485	458	34	4	1	456	34952598	34952144	2.270000e-175	625.0
3	TraesCS2B01G068300	chr2B	84.807	362	45	6	141	495	24905133	24905491	3.290000e-94	355.0
4	TraesCS2B01G068300	chr2D	90.827	2660	178	30	1	2645	21641512	21644120	0.000000e+00	3500.0
5	TraesCS2B01G068300	chr2D	93.585	2120	113	12	1	2110	21680326	21682432	0.000000e+00	3140.0
6	TraesCS2B01G068300	chr2D	89.615	1868	138	18	831	2690	21620839	21622658	0.000000e+00	2324.0
7	TraesCS2B01G068300	chr2D	93.253	1245	71	8	1	1242	21663911	21665145	0.000000e+00	1821.0
8	TraesCS2B01G068300	chr2D	85.252	556	49	17	2145	2687	21682429	21682964	2.360000e-150	542.0
9	TraesCS2B01G068300	chr2D	93.720	207	13	0	2481	2687	21666140	21666346	7.230000e-81	311.0
10	TraesCS2B01G068300	chr2D	96.262	107	4	0	735	841	21619526	21619632	2.750000e-40	176.0
11	TraesCS2B01G068300	chr2A	91.578	1983	146	11	64	2042	23877926	23879891	0.000000e+00	2717.0
12	TraesCS2B01G068300	chr2A	88.692	1866	175	23	546	2386	23827985	23829839	0.000000e+00	2244.0
13	TraesCS2B01G068300	chr2A	89.580	547	55	2	2145	2690	23879997	23880542	0.000000e+00	693.0
14	TraesCS2B01G068300	chr2A	97.101	69	2	0	1	69	23866089	23866157	1.690000e-22	117.0
15	TraesCS2B01G068300	chr2A	97.727	44	1	0	705	748	23828187	23828230	2.870000e-10	76.8
16	TraesCS2B01G068300	chr6A	82.482	1233	147	34	776	1971	604573922	604572722	0.000000e+00	1016.0
17	TraesCS2B01G068300	chr6A	79.954	1297	191	41	704	1971	604456213	604454957	0.000000e+00	891.0
18	TraesCS2B01G068300	chr6A	95.000	40	2	0	794	833	604458341	604458302	2.240000e-06	63.9
19	TraesCS2B01G068300	chr6D	81.818	1232	161	36	776	1971	457636689	457635485	0.000000e+00	976.0
20	TraesCS2B01G068300	chr3D	86.104	367	43	7	141	499	454744145	454744511	3.250000e-104	388.0
21	TraesCS2B01G068300	chrUn	85.753	365	40	8	141	495	61736694	61736332	2.530000e-100	375.0
22	TraesCS2B01G068300	chr1D	84.848	363	48	7	139	495	442791418	442791779	2.550000e-95	359.0
23	TraesCS2B01G068300	chr6B	91.071	112	8	2	1969	2078	695949746	695949857	1.670000e-32	150.0

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	TraesCS2B01G068300	chr2B	34862763	34865452	2689	True	4968.00	4968	100.0000	1	2690	1	chr2B.!!$R1	2689
1	TraesCS2B01G068300	chr2B	34888391	34890326	1935	True	2313.00	2313	88.3380	451	2386	1	chr2B.!!$R2	1935
2	TraesCS2B01G068300	chr2D	21641512	21644120	2608	False	3500.00	3500	90.8270	1	2645	1	chr2D.!!$F1	2644
3	TraesCS2B01G068300	chr2D	21680326	21682964	2638	False	1841.00	3140	89.4185	1	2687	2	chr2D.!!$F4	2686
4	TraesCS2B01G068300	chr2D	21619526	21622658	3132	False	1250.00	2324	92.9385	735	2690	2	chr2D.!!$F2	1955
5	TraesCS2B01G068300	chr2D	21663911	21666346	2435	False	1066.00	1821	93.4865	1	2687	2	chr2D.!!$F3	2686
6	TraesCS2B01G068300	chr2A	23877926	23880542	2616	False	1705.00	2717	90.5790	64	2690	2	chr2A.!!$F3	2626
7	TraesCS2B01G068300	chr2A	23827985	23829839	1854	False	1160.40	2244	93.2095	546	2386	2	chr2A.!!$F2	1840
8	TraesCS2B01G068300	chr6A	604572722	604573922	1200	True	1016.00	1016	82.4820	776	1971	1	chr6A.!!$R1	1195
9	TraesCS2B01G068300	chr6A	604454957	604458341	3384	True	477.45	891	87.4770	704	1971	2	chr6A.!!$R2	1267
10	TraesCS2B01G068300	chr6D	457635485	457636689	1204	True	976.00	976	81.8180	776	1971	1	chr6D.!!$R1	1195

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
52	53	0.246360	TATGGTGTGAGTGCGTCTGG	59.754	55.0	0.0	0.0	0.0	3.86	F
1112	3798	0.251916	CCGCCAATGACTACCAAGGA	59.748	55.0	0.0	0.0	0.0	3.36	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1302	3991	0.529773	GGCGACCAACGATGCTATCA	60.530	55.0	0.00	0.0	45.77	2.15	R
2129	4872	0.171679	AATGTGTGATGCATGGCACG	59.828	50.0	19.18	0.0	43.04	5.34	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
47	48	1.290203	GATGGTATGGTGTGAGTGCG	58.710	55.000	0.00	0.00	0.00	5.34
52	53	0.246360	TATGGTGTGAGTGCGTCTGG	59.754	55.000	0.00	0.00	0.00	3.86
304	306	0.890683	GCCAATGTTGACTTCAGGGG	59.109	55.000	0.00	0.00	0.00	4.79
312	315	4.803452	TGTTGACTTCAGGGGAAAAAGAT	58.197	39.130	0.00	0.00	31.35	2.40
524	528	1.271871	ACGCCCAGGAATCAAACATCA	60.272	47.619	0.00	0.00	0.00	3.07
526	530	2.230992	CGCCCAGGAATCAAACATCAAA	59.769	45.455	0.00	0.00	0.00	2.69
527	531	3.588955	GCCCAGGAATCAAACATCAAAC	58.411	45.455	0.00	0.00	0.00	2.93
659	692	3.550436	CGCGGTAGATCTAAGGAGGAAAC	60.550	52.174	3.40	0.00	0.00	2.78
671	704	8.120140	TCTAAGGAGGAAACTAACTTGAGTAC	57.880	38.462	0.00	0.00	44.43	2.73
695	728	4.119442	AGTGGCGTACTTACATACAAGG	57.881	45.455	0.00	0.00	35.67	3.61
848	3507	0.543277	TGTAGAGCCCTTCAGCATGG	59.457	55.000	0.00	0.00	36.16	3.66
873	3537	7.439655	GGAGCAATACCAAGTAAGACTAATCAG	59.560	40.741	0.00	0.00	0.00	2.90
874	3538	7.852263	AGCAATACCAAGTAAGACTAATCAGT	58.148	34.615	0.00	0.00	37.87	3.41
904	3571	5.440610	ACCTAGCTAATTTGGACATTGGAG	58.559	41.667	3.87	0.00	0.00	3.86
962	3631	4.276183	GCTACTTGTCGATCAGTATGGAGA	59.724	45.833	7.03	0.00	36.16	3.71
983	3652	4.710375	AGAACGCATTCCTACTTTCCTAGA	59.290	41.667	0.00	0.00	35.18	2.43
984	3653	5.187186	AGAACGCATTCCTACTTTCCTAGAA	59.813	40.000	0.00	0.00	35.18	2.10
998	3684	7.379750	ACTTTCCTAGAAAGCACAGTAAGTAG	58.620	38.462	15.25	0.00	0.00	2.57
1070	3756	0.391597	ACCAACGAGGACGACAATGT	59.608	50.000	5.70	0.00	42.66	2.71
1112	3798	0.251916	CCGCCAATGACTACCAAGGA	59.748	55.000	0.00	0.00	0.00	3.36
1221	3910	1.147600	GTCCTTCACCAACCACGGT	59.852	57.895	0.00	0.00	41.07	4.83
1302	3991	2.301583	GTGCCTCTTCTTCTCCTTCACT	59.698	50.000	0.00	0.00	0.00	3.41
1383	4072	3.309954	GCTTCAACGTGTTCAACTTCTCT	59.690	43.478	0.00	0.00	0.00	3.10
1458	4147	2.892425	CGGCCGCTGGACTTCATC	60.892	66.667	14.67	0.00	0.00	2.92
1536	4225	3.347077	CAGAACTGCTTCTTCCCAGAT	57.653	47.619	0.00	0.00	34.20	2.90
1560	4249	0.603975	GCAGGAACACCGAAGAGCTT	60.604	55.000	0.00	0.00	0.00	3.74
1623	4312	2.108075	TGTGTTCATCATGTTCCCCACT	59.892	45.455	0.00	0.00	0.00	4.00
1820	4512	2.524394	ACACCACTCCTCGCAGGT	60.524	61.111	2.68	0.00	36.53	4.00
1908	4607	1.267806	GTCTGCCATGGTTGTCTTGTG	59.732	52.381	14.67	0.00	0.00	3.33
1921	4620	6.099341	GGTTGTCTTGTGAACAAAGAAATGT	58.901	36.000	0.00	0.00	35.15	2.71
1922	4621	6.589907	GGTTGTCTTGTGAACAAAGAAATGTT	59.410	34.615	0.00	0.00	45.82	2.71
1923	4622	7.117667	GGTTGTCTTGTGAACAAAGAAATGTTT	59.882	33.333	0.00	0.00	43.31	2.83
1962	4661	5.650266	CAGGTGTAAAATTATGTAGGTGCCA	59.350	40.000	0.00	0.00	0.00	4.92
1967	4666	5.596836	AAAATTATGTAGGTGCCATGTGG	57.403	39.130	0.00	0.00	38.53	4.17
2031	4733	5.092554	TGAGCGGAAATAATACAAGGACA	57.907	39.130	0.00	0.00	0.00	4.02
2051	4788	8.918202	AGGACAAAACTCATCAAGTAATGTTA	57.082	30.769	0.00	0.00	37.16	2.41
2108	4851	4.388773	TGCATTTTACTTCTGTGCTAGACG	59.611	41.667	0.00	0.00	36.78	4.18
2120	4863	1.067071	TGCTAGACGTCGAGAGAGTGA	60.067	52.381	27.16	2.55	43.49	3.41
2122	4865	1.928503	CTAGACGTCGAGAGAGTGACC	59.071	57.143	19.67	0.00	43.49	4.02
2129	4872	1.000163	TCGAGAGAGTGACCTGTTTGC	60.000	52.381	0.00	0.00	34.84	3.68
2133	4876	1.160329	AGAGTGACCTGTTTGCGTGC	61.160	55.000	0.00	0.00	0.00	5.34
2146	4889	2.980378	GCGTGCCATGCATCACACA	61.980	57.895	22.13	6.44	41.91	3.72
2214	4995	7.173218	TGCTAAAGACTTTCTTACTCATGGTTG	59.827	37.037	3.07	0.00	35.27	3.77
2232	5013	4.019411	TGGTTGATGAAGAATGTGCTAGGA	60.019	41.667	0.00	0.00	0.00	2.94
2253	5034	0.584396	GTCGTGTCAATGCACCGAAA	59.416	50.000	0.00	0.00	36.08	3.46
2262	5043	3.192422	TCAATGCACCGAAAATGGGTTAG	59.808	43.478	0.00	0.00	34.97	2.34
2303	5085	1.250328	TGCTCGAACGGAAAGAGGTA	58.750	50.000	0.00	0.00	32.96	3.08
2305	5087	1.469423	GCTCGAACGGAAAGAGGTAGG	60.469	57.143	0.00	0.00	32.96	3.18
2345	5131	9.586435	AGCTAAAGCACAATGTTATTTATTTCC	57.414	29.630	4.54	0.00	45.16	3.13
2346	5132	8.817100	GCTAAAGCACAATGTTATTTATTTCCC	58.183	33.333	0.00	0.00	41.59	3.97
2354	5140	9.737844	ACAATGTTATTTATTTCCCTTTGCAAT	57.262	25.926	0.00	0.00	0.00	3.56
2365	5151	2.137523	CCTTTGCAATGGAAGCACAAC	58.862	47.619	23.59	0.00	42.54	3.32
2435	5227	1.205657	GATGCGCAATGCCAAATCTG	58.794	50.000	17.11	0.00	45.60	2.90
2447	5239	3.320256	TGCCAAATCTGTGTGTTGCATAA	59.680	39.130	0.00	0.00	0.00	1.90
2466	5258	5.620654	GCATAACAGATGTGCATTTCACTGT	60.621	40.000	0.00	0.00	44.81	3.55
2477	5269	2.341846	TTTCACTGTTCAGGGTCACC	57.658	50.000	1.92	0.00	0.00	4.02
2516	5326	1.073025	GGCATGGTGGTGTCTGACA	59.927	57.895	6.36	6.36	0.00	3.58
2610	5424	6.016860	GCATGCAACTATGTCAATTCAGGATA	60.017	38.462	14.21	0.00	0.00	2.59
2645	5459	3.493767	AAGGCCTCGTTCTCTTTCTTT	57.506	42.857	5.23	0.00	0.00	2.52
2647	5461	2.635427	AGGCCTCGTTCTCTTTCTTTCT	59.365	45.455	0.00	0.00	0.00	2.52
2676	5490	0.417841	AGAGGACCCTTTGGCTAGGA	59.582	55.000	7.67	0.00	37.50	2.94

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
47	48	1.202770	AGCACCAAGTACAACCCAGAC	60.203	52.381	0.00	0.00	0.00	3.51
52	53	4.267349	TCTAGAAGCACCAAGTACAACC	57.733	45.455	0.00	0.00	0.00	3.77
150	151	6.594937	GGTGTATATACAACCAGGTTCGAAAA	59.405	38.462	18.58	0.00	37.94	2.29
285	287	0.890683	CCCCTGAAGTCAACATTGGC	59.109	55.000	0.00	0.00	0.00	4.52
611	615	9.149225	GTTCCAAATTACATTGCACATCAAATA	57.851	29.630	0.00	0.00	38.34	1.40
616	620	4.031652	GCGTTCCAAATTACATTGCACATC	59.968	41.667	0.00	0.00	0.00	3.06
659	692	4.056050	ACGCCACTTTGTACTCAAGTTAG	58.944	43.478	7.96	5.19	34.88	2.34
671	704	5.163893	CCTTGTATGTAAGTACGCCACTTTG	60.164	44.000	8.16	0.00	45.54	2.77
688	721	3.543680	ATGCTAGTCAACGCCTTGTAT	57.456	42.857	0.00	0.00	0.00	2.29
695	728	7.596749	ATTGGTAATATATGCTAGTCAACGC	57.403	36.000	0.00	0.00	0.00	4.84
732	2159	1.002087	ACCTGTGTAGTTAGCAGCCAC	59.998	52.381	0.00	0.00	0.00	5.01
848	3507	7.982354	ACTGATTAGTCTTACTTGGTATTGCTC	59.018	37.037	0.00	0.00	28.79	4.26
873	3537	1.379527	AATTAGCTAGGTTGGCGCAC	58.620	50.000	10.83	0.00	34.52	5.34
874	3538	1.742831	CAAATTAGCTAGGTTGGCGCA	59.257	47.619	10.83	0.00	34.52	6.09
904	3571	5.440610	ACACAGAAATCCTATGGGAATGAC	58.559	41.667	0.22	0.00	45.78	3.06
962	3631	5.416271	TTCTAGGAAAGTAGGAATGCGTT	57.584	39.130	0.00	0.00	0.00	4.84
983	3652	4.010349	GGCCATTCTACTTACTGTGCTTT	58.990	43.478	0.00	0.00	0.00	3.51
984	3653	3.264450	AGGCCATTCTACTTACTGTGCTT	59.736	43.478	5.01	0.00	0.00	3.91
998	3684	2.979240	ACGAAGAAGAAGAGGCCATTC	58.021	47.619	5.01	9.26	0.00	2.67
1221	3910	0.606604	GGTTGGAGGTCTCGCACTTA	59.393	55.000	0.00	0.00	0.00	2.24
1302	3991	0.529773	GGCGACCAACGATGCTATCA	60.530	55.000	0.00	0.00	45.77	2.15
1383	4072	1.152860	CTGCCTCTCCTCCTCGCTA	60.153	63.158	0.00	0.00	0.00	4.26
1533	4222	1.001641	GGTGTTCCTGCTGGCATCT	60.002	57.895	4.42	0.00	0.00	2.90
1536	4225	3.113514	TTCGGTGTTCCTGCTGGCA	62.114	57.895	4.42	0.00	0.00	4.92
1560	4249	3.008835	CCCATTGGCAGATTCTTGAGA	57.991	47.619	0.00	0.00	0.00	3.27
1623	4312	3.788142	AGAATCCAATGCCCTTCCTCTTA	59.212	43.478	0.00	0.00	0.00	2.10
1763	4455	9.753674	TGAGTACAAATTTCCTGAAGGATTTAT	57.246	29.630	0.00	0.00	44.98	1.40
1820	4512	4.721776	AGATACAATCAAGCCCCTTCTACA	59.278	41.667	0.00	0.00	0.00	2.74
1857	4549	8.579850	ACATGGATACTTCACAAATTACATGT	57.420	30.769	2.69	2.69	39.97	3.21
1877	4572	1.471287	CATGGCAGACACTGAACATGG	59.529	52.381	19.22	8.76	40.84	3.66
1928	4627	8.200792	ACATAATTTTACACCTGCTTTTGACAA	58.799	29.630	0.00	0.00	0.00	3.18
1940	4639	6.096282	ACATGGCACCTACATAATTTTACACC	59.904	38.462	0.00	0.00	0.00	4.16
2051	4788	3.046283	TGGCAGAGGTATGTGGATACT	57.954	47.619	0.00	0.00	35.63	2.12
2108	4851	2.667137	CAAACAGGTCACTCTCTCGAC	58.333	52.381	0.00	0.00	0.00	4.20
2120	4863	3.041701	CATGGCACGCAAACAGGT	58.958	55.556	0.00	0.00	0.00	4.00
2122	4865	1.074319	GATGCATGGCACGCAAACAG	61.074	55.000	13.86	0.00	43.04	3.16
2129	4872	0.171679	AATGTGTGATGCATGGCACG	59.828	50.000	19.18	0.00	43.04	5.34
2175	4956	7.986085	AAGTCTTTAGCAACAATAGACACAT	57.014	32.000	0.00	0.00	38.11	3.21
2194	4975	7.009179	TCATCAACCATGAGTAAGAAAGTCT	57.991	36.000	0.00	0.00	39.39	3.24
2205	4986	4.398358	AGCACATTCTTCATCAACCATGAG	59.602	41.667	0.00	0.00	42.76	2.90
2214	4995	4.447054	CGACATCCTAGCACATTCTTCATC	59.553	45.833	0.00	0.00	0.00	2.92
2232	5013	0.320334	TCGGTGCATTGACACGACAT	60.320	50.000	0.00	0.00	41.65	3.06
2253	5034	2.279935	TTCGGTGCAACTAACCCATT	57.720	45.000	0.00	0.00	36.74	3.16
2277	5058	1.779569	TTCCGTTCGAGCAAGAAGTC	58.220	50.000	0.00	0.00	0.00	3.01
2278	5059	2.135933	CTTTCCGTTCGAGCAAGAAGT	58.864	47.619	0.00	0.00	0.00	3.01
2303	5085	7.281100	GTGCTTTAGCTTCTATCAAATGTACCT	59.719	37.037	0.00	0.00	42.66	3.08
2305	5087	7.974675	TGTGCTTTAGCTTCTATCAAATGTAC	58.025	34.615	0.00	0.00	42.66	2.90
2345	5131	2.137523	GTTGTGCTTCCATTGCAAAGG	58.862	47.619	14.62	14.62	42.41	3.11
2346	5132	2.540931	GTGTTGTGCTTCCATTGCAAAG	59.459	45.455	1.71	0.00	42.41	2.77
2354	5140	4.713553	TCAAGAATAGTGTTGTGCTTCCA	58.286	39.130	0.00	0.00	30.16	3.53
2391	5177	1.942677	ATTCACACGAACCGTTGTCA	58.057	45.000	0.00	0.00	38.32	3.58
2393	5179	3.430895	GTGATATTCACACGAACCGTTGT	59.569	43.478	2.85	0.00	46.22	3.32
2394	5180	3.986128	GTGATATTCACACGAACCGTTG	58.014	45.455	2.85	0.00	46.22	4.10
2435	5227	3.236816	GCACATCTGTTATGCAACACAC	58.763	45.455	0.00	0.00	39.75	3.82
2466	5258	0.323633	CATGGCATGGTGACCCTGAA	60.324	55.000	19.80	0.00	0.00	3.02
2477	5269	3.065786	CCTGTAAACACTAGCATGGCATG	59.934	47.826	22.99	22.99	0.00	4.06
2516	5326	1.877443	GATTACACCACAACGGCAACT	59.123	47.619	0.00	0.00	39.03	3.16
2582	5392	6.238814	CCTGAATTGACATAGTTGCATGCATA	60.239	38.462	23.37	12.62	0.00	3.14
2583	5393	5.451381	CCTGAATTGACATAGTTGCATGCAT	60.451	40.000	23.37	10.46	0.00	3.96
2584	5394	4.142337	CCTGAATTGACATAGTTGCATGCA	60.142	41.667	18.46	18.46	0.00	3.96
2585	5395	4.096833	TCCTGAATTGACATAGTTGCATGC	59.903	41.667	11.82	11.82	0.00	4.06
2610	5424	6.424032	ACGAGGCCTTTATTCCTTTTCTAAT	58.576	36.000	6.77	0.00	31.71	1.73
2645	5459	0.608640	GGTCCTCTTTCTTCCGCAGA	59.391	55.000	0.00	0.00	0.00	4.26
2647	5461	0.836400	AGGGTCCTCTTTCTTCCGCA	60.836	55.000	0.00	0.00	0.00	5.69

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.