AutoCloner

Multiple sequence alignment - TraesCS5A01G336200

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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	TraesCS5A01G336200	chr5A	100.000	2491	0	0	1	2491	545074657	545077147	0.000000e+00	4601.0
1	TraesCS5A01G336200	chr5A	85.827	508	66	6	1988	2491	260022857	260022352	3.650000e-148	534.0
2	TraesCS5A01G336200	chr5A	84.211	418	39	11	401	810	545059971	545060369	5.030000e-102	381.0
3	TraesCS5A01G336200	chr5A	92.015	263	16	4	1331	1592	545060714	545060972	5.060000e-97	364.0
4	TraesCS5A01G336200	chr5A	85.124	363	26	16	1	345	545059623	545059975	1.830000e-91	346.0
5	TraesCS5A01G336200	chr5D	93.981	1977	64	22	51	1981	429290435	429292402	0.000000e+00	2940.0
6	TraesCS5A01G336200	chr5D	85.427	398	29	12	3	380	423009265	423008877	1.080000e-103	387.0
7	TraesCS5A01G336200	chr5B	93.843	1608	51	18	1	1592	518482453	518484028	0.000000e+00	2377.0
8	TraesCS5A01G336200	chr5B	88.116	690	54	13	917	1589	518474858	518475536	0.000000e+00	795.0
9	TraesCS5A01G336200	chr5B	85.000	400	29	14	1	380	310664183	310663795	6.500000e-101	377.0
10	TraesCS5A01G336200	chr5B	95.089	224	6	2	1587	1805	518484065	518484288	5.100000e-92	348.0
11	TraesCS5A01G336200	chr5B	92.857	154	7	3	1835	1984	518484281	518484434	1.160000e-53	220.0
12	TraesCS5A01G336200	chr7D	80.643	1679	185	64	1	1589	2038029	2036401	0.000000e+00	1171.0
13	TraesCS5A01G336200	chr4A	79.976	1673	188	82	1	1589	742607425	742605816	0.000000e+00	1098.0
14	TraesCS5A01G336200	chr4A	97.368	38	1	0	431	468	742651143	742651106	5.750000e-07	65.8
15	TraesCS5A01G336200	chrUn	81.646	1215	121	45	158	1311	81435328	81436501	0.000000e+00	915.0
16	TraesCS5A01G336200	chrUn	81.646	1215	121	45	158	1311	336021890	336023063	0.000000e+00	915.0
17	TraesCS5A01G336200	chrUn	85.427	398	25	14	1	376	423143791	423143405	1.400000e-102	383.0
18	TraesCS5A01G336200	chr2A	90.570	509	45	3	1986	2491	4801627	4802135	0.000000e+00	671.0
19	TraesCS5A01G336200	chr2A	85.279	394	28	13	3	376	557968585	557968968	1.810000e-101	379.0
20	TraesCS5A01G336200	chr2A	84.264	394	32	13	3	376	332987117	332986734	8.470000e-95	357.0
21	TraesCS5A01G336200	chr6D	86.982	507	63	3	1988	2491	48674769	48675275	3.600000e-158	568.0
22	TraesCS5A01G336200	chr6D	85.464	399	24	15	1	376	429327267	429326880	3.890000e-103	385.0
23	TraesCS5A01G336200	chr1D	86.785	507	61	6	1989	2491	444329116	444329620	6.020000e-156	560.0
24	TraesCS5A01G336200	chr1D	86.733	505	58	8	1991	2491	285610623	285610124	1.010000e-153	553.0
25	TraesCS5A01G336200	chr1D	85.464	399	24	14	1	376	26172298	26172685	3.890000e-103	385.0
26	TraesCS5A01G336200	chr1D	85.427	398	25	14	1	376	319537181	319536795	1.400000e-102	383.0
27	TraesCS5A01G336200	chr1D	85.427	398	24	15	1	376	458737337	458737722	1.400000e-102	383.0
28	TraesCS5A01G336200	chr1D	85.000	400	24	19	1	376	319556392	319556005	8.410000e-100	374.0
29	TraesCS5A01G336200	chr6A	85.714	511	65	8	1986	2491	611336721	611336214	1.310000e-147	532.0
30	TraesCS5A01G336200	chr3A	85.630	508	67	6	1987	2491	693483340	693483844	1.700000e-146	529.0
31	TraesCS5A01G336200	chr3A	85.380	513	68	7	1983	2491	732236360	732236869	2.190000e-145	525.0
32	TraesCS5A01G336200	chr2D	85.271	516	71	5	1979	2491	624546861	624546348	6.100000e-146	527.0
33	TraesCS5A01G336200	chr4D	85.714	399	25	13	1	378	417844029	417843642	2.320000e-105	392.0
34	TraesCS5A01G336200	chr1A	85.533	394	27	13	3	376	291730557	291730940	3.890000e-103	385.0
35	TraesCS5A01G336200	chr1A	85.316	395	27	13	3	376	292014052	292014436	1.810000e-101	379.0
36	TraesCS5A01G336200	chr1A	85.025	394	28	14	3	376	293321442	293321060	3.030000e-99	372.0

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	TraesCS5A01G336200	chr5A	545074657	545077147	2490	False	4601.000000	4601	100.000000	1	2491	1	chr5A.!!$F1	2490
1	TraesCS5A01G336200	chr5A	260022352	260022857	505	True	534.000000	534	85.827000	1988	2491	1	chr5A.!!$R1	503
2	TraesCS5A01G336200	chr5A	545059623	545060972	1349	False	363.666667	381	87.116667	1	1592	3	chr5A.!!$F2	1591
3	TraesCS5A01G336200	chr5D	429290435	429292402	1967	False	2940.000000	2940	93.981000	51	1981	1	chr5D.!!$F1	1930
4	TraesCS5A01G336200	chr5B	518482453	518484434	1981	False	981.666667	2377	93.929667	1	1984	3	chr5B.!!$F2	1983
5	TraesCS5A01G336200	chr5B	518474858	518475536	678	False	795.000000	795	88.116000	917	1589	1	chr5B.!!$F1	672
6	TraesCS5A01G336200	chr7D	2036401	2038029	1628	True	1171.000000	1171	80.643000	1	1589	1	chr7D.!!$R1	1588
7	TraesCS5A01G336200	chr4A	742605816	742607425	1609	True	1098.000000	1098	79.976000	1	1589	1	chr4A.!!$R1	1588
8	TraesCS5A01G336200	chrUn	81435328	81436501	1173	False	915.000000	915	81.646000	158	1311	1	chrUn.!!$F1	1153
9	TraesCS5A01G336200	chrUn	336021890	336023063	1173	False	915.000000	915	81.646000	158	1311	1	chrUn.!!$F2	1153
10	TraesCS5A01G336200	chr2A	4801627	4802135	508	False	671.000000	671	90.570000	1986	2491	1	chr2A.!!$F1	505
11	TraesCS5A01G336200	chr6D	48674769	48675275	506	False	568.000000	568	86.982000	1988	2491	1	chr6D.!!$F1	503
12	TraesCS5A01G336200	chr1D	444329116	444329620	504	False	560.000000	560	86.785000	1989	2491	1	chr1D.!!$F2	502
13	TraesCS5A01G336200	chr6A	611336214	611336721	507	True	532.000000	532	85.714000	1986	2491	1	chr6A.!!$R1	505
14	TraesCS5A01G336200	chr3A	693483340	693483844	504	False	529.000000	529	85.630000	1987	2491	1	chr3A.!!$F1	504
15	TraesCS5A01G336200	chr3A	732236360	732236869	509	False	525.000000	525	85.380000	1983	2491	1	chr3A.!!$F2	508
16	TraesCS5A01G336200	chr2D	624546348	624546861	513	True	527.000000	527	85.271000	1979	2491	1	chr2D.!!$R1	512

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
717	809	0.035317	TGGCTGCTCAACTACCTGTG	59.965	55.0	0.0	0.0	0.0	3.66	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2071	2388	1.446792	CGAGCAAGCATCTCACGGT	60.447	57.895	0.0	0.0	0.0	4.83	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
153	176	9.953825	GAAAAATTACACAGATACTACAGAACG	57.046	33.333	0.00	0.00	0.00	3.95
160	183	6.024664	CACAGATACTACAGAACGAGTGAAG	58.975	44.000	0.00	0.00	0.00	3.02
617	688	3.116823	TGGAGGATGGATCTCAGATCTGT	60.117	47.826	21.92	3.10	33.18	3.41
711	803	2.224744	TGGAACAATGGCTGCTCAACTA	60.225	45.455	0.00	0.00	31.92	2.24
712	804	2.162408	GGAACAATGGCTGCTCAACTAC	59.838	50.000	0.00	0.00	0.00	2.73
713	805	1.826385	ACAATGGCTGCTCAACTACC	58.174	50.000	0.00	0.00	0.00	3.18
714	806	1.352352	ACAATGGCTGCTCAACTACCT	59.648	47.619	0.00	0.00	0.00	3.08
715	807	1.741706	CAATGGCTGCTCAACTACCTG	59.258	52.381	0.00	0.00	0.00	4.00
716	808	0.987294	ATGGCTGCTCAACTACCTGT	59.013	50.000	0.00	0.00	0.00	4.00
717	809	0.035317	TGGCTGCTCAACTACCTGTG	59.965	55.000	0.00	0.00	0.00	3.66
718	810	1.301677	GGCTGCTCAACTACCTGTGC	61.302	60.000	0.00	0.00	36.56	4.57
719	811	0.321122	GCTGCTCAACTACCTGTGCT	60.321	55.000	0.00	0.00	36.88	4.40
720	812	1.719600	CTGCTCAACTACCTGTGCTC	58.280	55.000	0.00	0.00	36.88	4.26
721	813	0.321671	TGCTCAACTACCTGTGCTCC	59.678	55.000	0.00	0.00	36.88	4.70
722	814	0.321671	GCTCAACTACCTGTGCTCCA	59.678	55.000	0.00	0.00	33.92	3.86
723	815	1.941668	GCTCAACTACCTGTGCTCCAC	60.942	57.143	0.00	0.00	33.92	4.02
724	816	1.344438	CTCAACTACCTGTGCTCCACA	59.656	52.381	0.00	0.00	42.45	4.17
725	817	1.765904	TCAACTACCTGTGCTCCACAA	59.234	47.619	0.00	0.00	44.08	3.33
726	818	2.371841	TCAACTACCTGTGCTCCACAAT	59.628	45.455	0.00	0.00	44.08	2.71
727	819	2.479566	ACTACCTGTGCTCCACAATG	57.520	50.000	0.00	0.00	44.08	2.82
728	820	1.699634	ACTACCTGTGCTCCACAATGT	59.300	47.619	0.00	3.17	44.08	2.71
746	840	5.182001	ACAATGTTCTGTGCTTGAGAATACC	59.818	40.000	0.00	0.00	32.18	2.73
811	905	8.186178	CTCACTTTTGAGGTACATACATACAC	57.814	38.462	0.00	0.00	45.06	2.90
850	1046	6.018262	TCACTCACACTGCTAATTAACACAAC	60.018	38.462	0.00	0.00	0.00	3.32
978	1208	8.470002	TCATCATACTCATCTTATAACCCATCG	58.530	37.037	0.00	0.00	0.00	3.84
1133	1384	2.640184	CACTGACTGTCATGATGCCAT	58.360	47.619	11.45	0.00	0.00	4.40
1139	1390	0.549469	TGTCATGATGCCATCCAGCT	59.451	50.000	0.00	0.00	0.00	4.24
1225	1476	5.415389	ACCGTTAGTAAGAAGAGAGAGGAAC	59.585	44.000	0.00	0.00	0.00	3.62
1345	1608	5.122328	GCAATTGATGCGAGTTTGAATTC	57.878	39.130	10.34	0.00	46.87	2.17
1634	1941	2.101582	GTCATGCCTAGGTAGACCACTG	59.898	54.545	11.31	0.00	38.89	3.66
1770	2082	5.944007	TGCATTCTTTTTAGGGAGGTACTTC	59.056	40.000	0.00	0.00	41.55	3.01
1875	2187	6.854496	AATCATGTATTTTCATGCATTGCC	57.146	33.333	6.12	0.00	43.18	4.52
1948	2262	1.452110	GTGTGCATGCCTGTGATGTA	58.548	50.000	16.68	0.00	0.00	2.29
1952	2266	4.096231	GTGTGCATGCCTGTGATGTAAATA	59.904	41.667	16.68	0.00	0.00	1.40
2029	2346	0.546122	AGTTGTGTCCCACTGCTCAA	59.454	50.000	0.00	0.00	35.11	3.02
2038	2355	1.606224	CCCACTGCTCAATTTTGCCAC	60.606	52.381	0.00	0.00	0.00	5.01
2064	2381	9.301153	CTAAAAGTTACAACTGCTCAAAAATGT	57.699	29.630	0.00	0.00	39.66	2.71
2071	2388	5.238432	ACAACTGCTCAAAAATGTCATCGTA	59.762	36.000	0.00	0.00	0.00	3.43
2158	2477	4.222366	TGCTCAAAAATGCCATTGGACATA	59.778	37.500	6.95	0.00	0.00	2.29
2183	2502	0.464735	TGTCAGGTCAAACCCGTTGG	60.465	55.000	0.00	0.00	39.75	3.77
2208	2527	8.584157	GGCCATGTTATATGACAAAAATATCCA	58.416	33.333	4.23	0.00	32.47	3.41
2222	2541	9.707957	ACAAAAATATCCATAGACCCACATTTA	57.292	29.630	0.00	0.00	0.00	1.40
2254	2574	9.948964	TTTCTATCTCACAATCATATGTATGGG	57.051	33.333	1.90	4.64	34.50	4.00
2329	2650	1.971149	TGGGATCAAGTGAGACCCAT	58.029	50.000	18.93	0.00	44.02	4.00
2377	2700	2.840038	AGCTGACATGTTGGTCCATAGA	59.160	45.455	0.00	0.00	36.97	1.98
2417	2740	6.726490	ATAGGGTAAACGAGATTTGAGCTA	57.274	37.500	0.00	0.00	0.00	3.32
2418	2741	5.012328	AGGGTAAACGAGATTTGAGCTAG	57.988	43.478	0.00	0.00	0.00	3.42
2431	2754	5.414789	TTTGAGCTAGCAGTAATGGTGTA	57.585	39.130	18.83	0.00	0.00	2.90
2438	2761	2.843730	AGCAGTAATGGTGTATGGTGGA	59.156	45.455	0.00	0.00	0.00	4.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
153	176	4.900635	TTTGTTTCTTGAGGCTTCACTC	57.099	40.909	0.00	0.00	37.99	3.51
382	430	2.279582	ACCTCTGTACAATTCGCTCG	57.720	50.000	0.00	0.00	0.00	5.03
426	474	5.049828	GGCTTTGTGTGCTAAAAATGAAGT	58.950	37.500	0.00	0.00	0.00	3.01
632	706	7.708752	CCTCTTTGATCTCCTACTATTGTTGTC	59.291	40.741	0.00	0.00	0.00	3.18
711	803	1.143684	AGAACATTGTGGAGCACAGGT	59.856	47.619	0.00	0.00	45.39	4.00
712	804	1.538512	CAGAACATTGTGGAGCACAGG	59.461	52.381	0.00	0.00	45.39	4.00
713	805	2.031420	CACAGAACATTGTGGAGCACAG	60.031	50.000	0.00	0.00	45.39	3.66
714	806	1.948834	CACAGAACATTGTGGAGCACA	59.051	47.619	0.00	0.00	43.65	4.57
715	807	1.335324	GCACAGAACATTGTGGAGCAC	60.335	52.381	8.08	0.00	46.62	4.40
716	808	0.953727	GCACAGAACATTGTGGAGCA	59.046	50.000	8.08	0.00	46.62	4.26
717	809	1.242076	AGCACAGAACATTGTGGAGC	58.758	50.000	8.08	1.62	46.62	4.70
718	810	2.880268	TCAAGCACAGAACATTGTGGAG	59.120	45.455	8.08	0.00	46.62	3.86
719	811	2.880268	CTCAAGCACAGAACATTGTGGA	59.120	45.455	8.08	0.00	46.62	4.02
720	812	2.880268	TCTCAAGCACAGAACATTGTGG	59.120	45.455	8.08	0.00	46.62	4.17
722	814	5.182001	GGTATTCTCAAGCACAGAACATTGT	59.818	40.000	0.00	0.00	32.65	2.71
723	815	5.181811	TGGTATTCTCAAGCACAGAACATTG	59.818	40.000	0.00	0.00	32.65	2.82
724	816	5.316167	TGGTATTCTCAAGCACAGAACATT	58.684	37.500	0.00	0.00	32.65	2.71
725	817	4.910195	TGGTATTCTCAAGCACAGAACAT	58.090	39.130	0.00	0.00	32.65	2.71
726	818	4.350368	TGGTATTCTCAAGCACAGAACA	57.650	40.909	0.00	0.00	32.65	3.18
727	819	5.392380	CCATTGGTATTCTCAAGCACAGAAC	60.392	44.000	0.00	0.00	32.65	3.01
728	820	4.701651	CCATTGGTATTCTCAAGCACAGAA	59.298	41.667	0.00	0.00	34.37	3.02
746	840	5.003160	TGATGACCAACAAGTACTCCATTG	58.997	41.667	0.00	1.32	0.00	2.82
811	905	1.337167	TGAGTGAGCGAATGAGTGGTG	60.337	52.381	0.00	0.00	0.00	4.17
850	1046	5.754890	GCCAAATAACTGGGATGCAAATTAG	59.245	40.000	0.00	0.00	36.92	1.73
885	1087	6.648725	GCCAAGAAATTAAACCAAGCAATGTA	59.351	34.615	0.00	0.00	0.00	2.29
978	1208	2.870372	GGCTGGCACGACAATGTC	59.130	61.111	2.75	2.75	0.00	3.06
1003	1236	2.730090	CGTTGCTCATGGATTGCAGAAC	60.730	50.000	0.00	0.00	38.01	3.01
1018	1266	2.410939	CGATGGATGATGATCGTTGCT	58.589	47.619	0.00	0.00	37.33	3.91
1225	1476	4.659172	TTGCTTGGCCCTGTCCCG	62.659	66.667	0.00	0.00	0.00	5.14
1345	1608	6.046885	ACCTGCAAAATTGTTTCAAATTCG	57.953	33.333	0.00	0.00	0.00	3.34
1543	1806	9.166173	TCTATATGCACAAGGAATGTAATATGC	57.834	33.333	0.00	0.00	41.46	3.14
1547	1812	8.213679	ACTGTCTATATGCACAAGGAATGTAAT	58.786	33.333	0.00	0.00	41.46	1.89
1548	1813	7.495606	CACTGTCTATATGCACAAGGAATGTAA	59.504	37.037	0.00	0.00	41.46	2.41
1549	1814	6.986231	CACTGTCTATATGCACAAGGAATGTA	59.014	38.462	0.00	0.00	41.46	2.29
1550	1815	5.819379	CACTGTCTATATGCACAAGGAATGT	59.181	40.000	0.00	0.00	45.34	2.71
1634	1941	3.563808	TGTATTTGTGTGCTGTGGAGAAC	59.436	43.478	0.00	0.00	0.00	3.01
1984	2301	6.828785	AGTGGCATAAGTGATAAAAACCCTAG	59.171	38.462	0.00	0.00	0.00	3.02
2029	2346	6.478673	GCAGTTGTAACTTTTAGTGGCAAAAT	59.521	34.615	0.00	0.00	37.08	1.82
2038	2355	9.301153	ACATTTTTGAGCAGTTGTAACTTTTAG	57.699	29.630	0.00	0.00	37.08	1.85
2071	2388	1.446792	CGAGCAAGCATCTCACGGT	60.447	57.895	0.00	0.00	0.00	4.83
2254	2574	2.290071	TGCTTACTCTTACAAGTGGGGC	60.290	50.000	0.00	0.00	0.00	5.80
2417	2740	2.843730	TCCACCATACACCATTACTGCT	59.156	45.455	0.00	0.00	0.00	4.24
2418	2741	3.275617	TCCACCATACACCATTACTGC	57.724	47.619	0.00	0.00	0.00	4.40
2431	2754	3.008157	TGCATGCTCAAAAATTCCACCAT	59.992	39.130	20.33	0.00	0.00	3.55
2438	2761	4.022416	TCGTTAGGTGCATGCTCAAAAATT	60.022	37.500	20.33	1.00	0.00	1.82

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.