AutoCloner

Multiple sequence alignment - TraesCS2A01G328300

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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	TraesCS2A01G328300	chr2A	100.000	2594	0	0	1	2594	559830755	559828162	0.000000e+00	4791.0
1	TraesCS2A01G328300	chr2A	95.562	676	30	0	932	1607	559749979	559749304	0.000000e+00	1083.0
2	TraesCS2A01G328300	chr2A	94.595	407	17	4	1	403	559750400	559749995	2.190000e-175	625.0
3	TraesCS2A01G328300	chr2A	90.323	248	23	1	529	775	560210065	560209818	8.950000e-85	324.0
4	TraesCS2A01G328300	chr2A	80.392	255	43	5	79	333	559742704	559742457	1.230000e-43	187.0
5	TraesCS2A01G328300	chr2D	90.638	1645	105	13	1	1605	427931690	427933325	0.000000e+00	2139.0
6	TraesCS2A01G328300	chr2D	89.897	1643	100	22	1	1605	427914219	427915833	0.000000e+00	2054.0
7	TraesCS2A01G328300	chr2D	89.503	1610	115	23	35	1607	427897120	427898712	0.000000e+00	1988.0
8	TraesCS2A01G328300	chr2D	91.720	1087	61	7	524	1607	427753038	427754098	0.000000e+00	1482.0
9	TraesCS2A01G328300	chr2D	83.137	848	99	25	716	1539	427925315	427926142	0.000000e+00	734.0
10	TraesCS2A01G328300	chr2D	82.803	849	100	26	716	1539	427909566	427910393	0.000000e+00	717.0
11	TraesCS2A01G328300	chr2D	81.958	848	109	23	716	1539	427944535	427945362	0.000000e+00	678.0
12	TraesCS2A01G328300	chr2B	91.974	1221	70	16	402	1607	504747608	504748815	0.000000e+00	1687.0
13	TraesCS2A01G328300	chr2B	96.964	988	30	0	1607	2594	87331862	87332849	0.000000e+00	1659.0
14	TraesCS2A01G328300	chr2B	92.970	825	50	5	787	1607	512372888	512372068	0.000000e+00	1195.0
15	TraesCS2A01G328300	chr2B	87.437	398	41	7	402	792	512373753	512373358	1.420000e-122	449.0
16	TraesCS2A01G328300	chr2B	84.639	319	33	10	3	308	504747211	504747526	1.170000e-78	303.0
17	TraesCS2A01G328300	chr2B	79.667	300	43	15	35	332	512366337	512366054	1.570000e-47	200.0
18	TraesCS2A01G328300	chr2B	82.514	183	25	7	1616	1794	25428882	25429061	1.240000e-33	154.0
19	TraesCS2A01G328300	chr2B	79.096	177	24	7	716	886	512364420	512364251	2.730000e-20	110.0
20	TraesCS2A01G328300	chr5B	94.800	1000	28	7	1618	2594	710168534	710169532	0.000000e+00	1537.0
21	TraesCS2A01G328300	chr5B	81.250	96	15	3	2500	2594	442685214	442685121	9.960000e-10	75.0
22	TraesCS2A01G328300	chr3B	93.202	1015	31	3	1618	2594	603827403	603826389	0.000000e+00	1458.0
23	TraesCS2A01G328300	chr3B	91.330	1015	49	6	1618	2594	596244012	596242999	0.000000e+00	1351.0
24	TraesCS2A01G328300	chr3B	77.723	202	38	7	2180	2379	693727043	693727239	1.630000e-22	117.0
25	TraesCS2A01G328300	chr3B	91.935	62	3	2	2519	2580	772446524	772446465	4.600000e-13	86.1
26	TraesCS2A01G328300	chr1B	86.797	765	48	17	1864	2594	684731888	684732633	0.000000e+00	804.0
27	TraesCS2A01G328300	chr1B	88.690	504	53	3	1880	2383	660469801	660470300	1.710000e-171	612.0
28	TraesCS2A01G328300	chr1B	90.789	76	7	0	1745	1820	684731806	684731881	4.570000e-18	102.0
29	TraesCS2A01G328300	chr7D	92.929	198	13	1	2398	2594	521890747	521890550	1.170000e-73	287.0
30	TraesCS2A01G328300	chr1A	98.734	79	1	0	2398	2476	588668547	588668469	9.680000e-30	141.0
31	TraesCS2A01G328300	chr1A	97.260	73	2	0	2522	2594	588668460	588668388	9.750000e-25	124.0
32	TraesCS2A01G328300	chr7B	81.928	166	21	6	2393	2557	565765365	565765208	5.820000e-27	132.0
33	TraesCS2A01G328300	chr1D	90.000	70	4	3	2397	2464	419068770	419068838	1.280000e-13	87.9
34	TraesCS2A01G328300	chr7A	82.353	85	12	3	2511	2594	118794787	118794705	1.290000e-08	71.3

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	TraesCS2A01G328300	chr2A	559828162	559830755	2593	True	4791.0	4791	100.0000	1	2594	1	chr2A.!!$R2	2593
1	TraesCS2A01G328300	chr2A	559749304	559750400	1096	True	854.0	1083	95.0785	1	1607	2	chr2A.!!$R4	1606
2	TraesCS2A01G328300	chr2D	427931690	427933325	1635	False	2139.0	2139	90.6380	1	1605	1	chr2D.!!$F4	1604
3	TraesCS2A01G328300	chr2D	427897120	427898712	1592	False	1988.0	1988	89.5030	35	1607	1	chr2D.!!$F2	1572
4	TraesCS2A01G328300	chr2D	427753038	427754098	1060	False	1482.0	1482	91.7200	524	1607	1	chr2D.!!$F1	1083
5	TraesCS2A01G328300	chr2D	427909566	427915833	6267	False	1385.5	2054	86.3500	1	1605	2	chr2D.!!$F6	1604
6	TraesCS2A01G328300	chr2D	427925315	427926142	827	False	734.0	734	83.1370	716	1539	1	chr2D.!!$F3	823
7	TraesCS2A01G328300	chr2D	427944535	427945362	827	False	678.0	678	81.9580	716	1539	1	chr2D.!!$F5	823
8	TraesCS2A01G328300	chr2B	87331862	87332849	987	False	1659.0	1659	96.9640	1607	2594	1	chr2B.!!$F2	987
9	TraesCS2A01G328300	chr2B	504747211	504748815	1604	False	995.0	1687	88.3065	3	1607	2	chr2B.!!$F3	1604
10	TraesCS2A01G328300	chr2B	512372068	512373753	1685	True	822.0	1195	90.2035	402	1607	2	chr2B.!!$R2	1205
11	TraesCS2A01G328300	chr5B	710168534	710169532	998	False	1537.0	1537	94.8000	1618	2594	1	chr5B.!!$F1	976
12	TraesCS2A01G328300	chr3B	603826389	603827403	1014	True	1458.0	1458	93.2020	1618	2594	1	chr3B.!!$R2	976
13	TraesCS2A01G328300	chr3B	596242999	596244012	1013	True	1351.0	1351	91.3300	1618	2594	1	chr3B.!!$R1	976
14	TraesCS2A01G328300	chr1B	684731806	684732633	827	False	453.0	804	88.7930	1745	2594	2	chr1B.!!$F2	849

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
551	5277	0.473755	ACTTGACCACATGTGCCTCA	59.526	50.0	20.81	18.28	34.02	3.86	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2112	7361	0.031616	TGCCAAGTTGGGGAAAACCT	60.032	50.0	23.36	0.0	38.19	3.5	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
54	4716	6.525629	AGATAATCCGAGTAATGGTTTGAGG	58.474	40.000	0.00	0.00	0.00	3.86
116	4780	3.610114	GCTGACATCATTGCTTTTGTCGT	60.610	43.478	0.00	0.00	41.02	4.34
151	4815	4.555313	CGCATATCGCTGGTGAATCATTTT	60.555	41.667	0.00	0.00	39.08	1.82
202	4869	6.787170	AGCATGTATGGTCTCATATGGAATT	58.213	36.000	2.13	0.00	38.06	2.17
308	4983	8.615878	TTGTTCGAGGAAAGATTAAATCAAGA	57.384	30.769	0.00	0.00	0.00	3.02
403	5083	2.185093	CGCCCCGTACAAGGTACC	59.815	66.667	2.73	2.73	0.00	3.34
404	5084	2.353610	CGCCCCGTACAAGGTACCT	61.354	63.158	9.21	9.21	0.00	3.08
406	5086	0.974525	GCCCCGTACAAGGTACCTCT	60.975	60.000	16.64	6.07	0.00	3.69
426	5133	2.749076	CTCCATCAATTGTCCGAAAGCA	59.251	45.455	5.13	0.00	0.00	3.91
478	5185	4.012895	CAACTTGCTTCCGCGCGT	62.013	61.111	29.95	3.84	39.65	6.01
551	5277	0.473755	ACTTGACCACATGTGCCTCA	59.526	50.000	20.81	18.28	34.02	3.86
611	5339	9.264719	CTTGAAATTTCAGGACTAAAAATGCTT	57.735	29.630	22.20	0.00	38.61	3.91
621	5349	7.004691	AGGACTAAAAATGCTTAGGTGTTTCT	58.995	34.615	0.00	0.00	33.85	2.52
638	5366	8.880244	AGGTGTTTCTAAGCATATATCACCATA	58.120	33.333	13.76	0.00	43.28	2.74
639	5367	9.155975	GGTGTTTCTAAGCATATATCACCATAG	57.844	37.037	8.72	0.61	41.34	2.23
684	5413	8.853077	TTTATGGACTCTAATCTATTGCCATG	57.147	34.615	0.00	0.00	36.40	3.66
758	5488	5.832060	TCAATTGGCCCATCAAATTTTGTTT	59.168	32.000	5.42	0.00	0.00	2.83
778	5508	9.979578	TTTGTTTTAATTGAGCACATGTTATCT	57.020	25.926	0.00	0.00	0.00	1.98
784	5514	2.760650	TGAGCACATGTTATCTCCGACT	59.239	45.455	13.76	0.00	0.00	4.18
785	5990	3.195610	TGAGCACATGTTATCTCCGACTT	59.804	43.478	13.76	0.00	0.00	3.01
831	6036	2.012673	CCATCTGTACTTGGCTTCTGC	58.987	52.381	0.00	0.00	38.76	4.26
863	6075	5.704354	TGTCATTAATGCCAACCCATCTAT	58.296	37.500	10.76	0.00	0.00	1.98
888	6108	2.671682	GGAGCAGGTCCTCCCAAC	59.328	66.667	11.76	0.00	44.60	3.77
921	6157	3.181461	CCAGGGCATAATCGAACTCTCTT	60.181	47.826	0.00	0.00	0.00	2.85
987	6227	3.280295	CTCTCCTAGGCTACAACTTCGA	58.720	50.000	2.96	0.00	0.00	3.71
1026	6266	1.338136	ACCCTAATCTGACAGCCGGG	61.338	60.000	2.18	13.37	36.30	5.73
1035	6275	1.301165	GACAGCCGGGTACGTGTTT	60.301	57.895	5.47	0.00	38.78	2.83
1049	6289	2.203437	GTTTCAACCCACCGGCCT	60.203	61.111	0.00	0.00	0.00	5.19
1117	6357	0.181114	CATCTTCCCCGGCTTCATCA	59.819	55.000	0.00	0.00	0.00	3.07
1119	6359	0.035439	TCTTCCCCGGCTTCATCAAC	60.035	55.000	0.00	0.00	0.00	3.18
1120	6360	0.322456	CTTCCCCGGCTTCATCAACA	60.322	55.000	0.00	0.00	0.00	3.33
1182	6422	3.560453	CCTTCCGGGAAAACCACATAAGA	60.560	47.826	11.24	0.00	40.22	2.10
1203	6443	1.628846	GATTATGGCGAGGTATGGGGT	59.371	52.381	0.00	0.00	0.00	4.95
1223	6463	0.884704	TTCTTCTTCGCGGCAAAGCT	60.885	50.000	6.13	0.00	34.40	3.74
1553	6799	2.438614	CGACAGCGAGGAGGAGGA	60.439	66.667	0.00	0.00	40.82	3.71
1556	6802	0.968393	GACAGCGAGGAGGAGGACTT	60.968	60.000	0.00	0.00	0.00	3.01
1588	6837	0.034896	GGTGTTGAAGAGGAAGCGGA	59.965	55.000	0.00	0.00	0.00	5.54
1612	6861	6.842163	ACGTAGAATTATGCAACTGGAAAAG	58.158	36.000	0.00	0.00	0.00	2.27
2131	7380	0.031616	AGGTTTTCCCCAACTTGGCA	60.032	50.000	1.76	0.00	41.86	4.92
2392	7646	0.603707	CTGTCAGCGTTGATGGGTGT	60.604	55.000	4.92	0.00	35.39	4.16

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
116	4780	1.401018	CGATATGCGTGCGTCTATGGA	60.401	52.381	0.00	0.00	34.64	3.41
202	4869	6.039605	CAGCATGGTCACATTCCACATATTTA	59.960	38.462	0.00	0.00	37.81	1.40
206	4874	3.054508	TCAGCATGGTCACATTCCACATA	60.055	43.478	0.00	0.00	37.81	2.29
220	4893	1.584175	GTCAGATGAGCTCAGCATGG	58.416	55.000	31.80	20.60	36.16	3.66
308	4983	5.536161	AGAGGTGCTTGTTGAACATATTTGT	59.464	36.000	0.00	0.00	37.82	2.83
320	4995	4.586001	ACAATTGATGAAGAGGTGCTTGTT	59.414	37.500	13.59	0.00	36.83	2.83
403	5083	3.064545	GCTTTCGGACAATTGATGGAGAG	59.935	47.826	13.59	10.64	0.00	3.20
404	5084	3.009723	GCTTTCGGACAATTGATGGAGA	58.990	45.455	13.59	1.38	0.00	3.71
406	5086	2.789213	TGCTTTCGGACAATTGATGGA	58.211	42.857	13.59	2.77	0.00	3.41
426	5133	1.344114	AGTTGTTGGCAAATCCGCATT	59.656	42.857	0.00	0.00	36.22	3.56
478	5185	4.047196	CCCCCTCCCCACCCCTTA	62.047	72.222	0.00	0.00	0.00	2.69
505	5229	4.747540	TTTTGAGGTTGATGATGACGTG	57.252	40.909	0.00	0.00	0.00	4.49
579	5305	9.799106	TTTTAGTCCTGAAATTTCAAGAGAGAT	57.201	29.630	20.82	11.74	36.64	2.75
596	5322	7.004691	AGAAACACCTAAGCATTTTTAGTCCT	58.995	34.615	0.00	0.00	0.00	3.85
611	5339	8.257602	TGGTGATATATGCTTAGAAACACCTA	57.742	34.615	21.92	13.04	43.49	3.08
662	5391	6.183361	ACACATGGCAATAGATTAGAGTCCAT	60.183	38.462	0.00	0.00	33.73	3.41
684	5413	2.027460	CGTGCTTGGCCCAAACAC	59.973	61.111	18.06	18.06	37.17	3.32
758	5488	6.257849	GTCGGAGATAACATGTGCTCAATTAA	59.742	38.462	19.23	3.78	40.67	1.40
778	5508	4.607239	AGAGGGTGTCTAATTAAGTCGGA	58.393	43.478	0.00	0.00	31.71	4.55
784	5514	9.132923	CACACTAGATAGAGGGTGTCTAATTAA	57.867	37.037	0.00	0.00	41.31	1.40
785	5990	7.230913	GCACACTAGATAGAGGGTGTCTAATTA	59.769	40.741	7.58	0.00	41.31	1.40
831	6036	3.763360	TGGCATTAATGACAGGAAGGTTG	59.237	43.478	20.34	0.00	41.84	3.77
863	6075	3.957288	GGACCTGCTCCTGCTTTTA	57.043	52.632	0.00	0.00	40.48	1.52
888	6108	4.939255	ATTATGCCCTGGGATAATTCAGG	58.061	43.478	19.27	4.30	43.36	3.86
893	6113	4.289672	AGTTCGATTATGCCCTGGGATAAT	59.710	41.667	19.27	19.21	46.68	1.28
921	6157	5.752036	AATGTTGAGTGGATCTGAGAGAA	57.248	39.130	0.00	0.00	0.00	2.87
1026	6266	0.582960	CGGTGGGTTGAAACACGTAC	59.417	55.000	0.00	0.00	38.46	3.67
1035	6275	3.172106	TCAAGGCCGGTGGGTTGA	61.172	61.111	1.90	4.56	34.97	3.18
1049	6289	1.476891	GGTAGTGGTCGATGAGCTCAA	59.523	52.381	22.50	0.40	0.00	3.02
1117	6357	2.280592	GACGTCCACGCCCTTGTT	60.281	61.111	3.51	0.00	44.43	2.83
1119	6359	2.030562	AAGACGTCCACGCCCTTG	59.969	61.111	13.01	0.00	44.43	3.61
1120	6360	2.030562	CAAGACGTCCACGCCCTT	59.969	61.111	13.01	0.54	44.43	3.95
1182	6422	1.909302	CCCCATACCTCGCCATAATCT	59.091	52.381	0.00	0.00	0.00	2.40
1203	6443	0.040425	GCTTTGCCGCGAAGAAGAAA	60.040	50.000	22.45	0.00	0.00	2.52
1272	6512	2.499685	GGCTTCTCCGTGCCGTAT	59.500	61.111	0.00	0.00	39.71	3.06
1519	6765	4.385405	GCTGGAGCTGCTGTCGGT	62.385	66.667	7.01	0.00	38.21	4.69
1553	6799	2.185350	CCATGGAGCGCTCGAAGT	59.815	61.111	29.81	10.59	0.00	3.01
1556	6802	2.942796	AACACCATGGAGCGCTCGA	61.943	57.895	29.81	27.32	0.00	4.04
1588	6837	6.128007	CCTTTTCCAGTTGCATAATTCTACGT	60.128	38.462	0.00	0.00	0.00	3.57
1853	7102	1.375908	CTAGAGGCCGCTGCACAAA	60.376	57.895	20.53	0.00	40.13	2.83
2112	7361	0.031616	TGCCAAGTTGGGGAAAACCT	60.032	50.000	23.36	0.00	38.19	3.50
2131	7380	2.025418	ACGCCGAGAAAACGCGAAT	61.025	52.632	15.93	0.00	36.92	3.34
2271	7525	0.811281	CCAAGGATTTTGCCGACCTC	59.189	55.000	0.00	0.00	31.89	3.85
2392	7646	2.733301	CATGGCCGCCACAAACAA	59.267	55.556	16.16	0.00	35.80	2.83

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.