AutoCloner

Multiple sequence alignment - TraesCS4B01G272800

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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	TraesCS4B01G272800	chr4B	100.000	2895	0	0	1	2895	550501807	550504701	0.000000e+00	5347.0
1	TraesCS4B01G272800	chr4B	87.712	1416	134	17	632	2033	550433451	550432062	0.000000e+00	1615.0
2	TraesCS4B01G272800	chr4B	92.803	931	61	3	1189	2113	550487576	550486646	0.000000e+00	1343.0
3	TraesCS4B01G272800	chr4B	85.558	914	125	6	986	1894	547309457	547310368	0.000000e+00	950.0
4	TraesCS4B01G272800	chr4B	89.013	537	46	9	657	1193	550488284	550487761	0.000000e+00	652.0
5	TraesCS4B01G272800	chr4B	82.511	223	21	11	1	221	550433909	550433703	2.290000e-41	180.0
6	TraesCS4B01G272800	chr4B	96.053	76	3	0	221	296	550489237	550489162	1.090000e-24	124.0
7	TraesCS4B01G272800	chr4D	92.578	2048	108	18	99	2120	442395158	442397187	0.000000e+00	2900.0
8	TraesCS4B01G272800	chr4D	91.683	1551	95	21	575	2116	442223441	442221916	0.000000e+00	2119.0
9	TraesCS4B01G272800	chr4D	89.450	1564	117	25	574	2120	442249242	442247710	0.000000e+00	1930.0
10	TraesCS4B01G272800	chr4D	86.361	1591	141	43	473	2033	442215873	442214329	0.000000e+00	1666.0
11	TraesCS4B01G272800	chr4D	85.246	915	127	8	986	1894	441255867	441256779	0.000000e+00	935.0
12	TraesCS4B01G272800	chr4D	82.960	223	20	8	1	221	442216347	442216141	4.930000e-43	185.0
13	TraesCS4B01G272800	chr4D	94.286	105	4	1	1	103	442389722	442389826	2.990000e-35	159.0
14	TraesCS4B01G272800	chr4D	78.802	217	19	12	221	411	442249564	442249349	1.410000e-23	121.0
15	TraesCS4B01G272800	chr4D	96.078	51	2	0	222	272	442224024	442223974	1.850000e-12	84.2
16	TraesCS4B01G272800	chr4D	90.909	44	4	0	1	44	442251102	442251059	3.120000e-05	60.2
17	TraesCS4B01G272800	chr4A	90.866	1675	115	13	462	2123	24919987	24918338	0.000000e+00	2211.0
18	TraesCS4B01G272800	chr4A	90.041	1466	109	18	576	2033	24935155	24936591	0.000000e+00	1864.0
19	TraesCS4B01G272800	chr4A	85.714	560	73	6	2339	2894	131994515	131993959	4.160000e-163	584.0
20	TraesCS4B01G272800	chr4A	92.208	77	6	0	2161	2237	24918338	24918262	3.050000e-20	110.0
21	TraesCS4B01G272800	chr5D	81.123	1282	161	43	657	1894	544798751	544799995	0.000000e+00	952.0
22	TraesCS4B01G272800	chr5D	94.737	38	2	0	230	267	544810929	544810966	3.120000e-05	60.2
23	TraesCS4B01G272800	chr2B	95.722	561	23	1	2335	2894	96227413	96226853	0.000000e+00	902.0
24	TraesCS4B01G272800	chr5B	79.827	1274	186	41	657	1894	687223392	687224630	0.000000e+00	863.0
25	TraesCS4B01G272800	chr5B	83.986	562	81	9	2321	2881	462728457	462729010	5.490000e-147	531.0
26	TraesCS4B01G272800	chr5B	80.606	330	28	15	848	1167	687259492	687259795	3.750000e-54	222.0
27	TraesCS4B01G272800	chr1A	90.374	561	53	1	2335	2894	486760540	486759980	0.000000e+00	736.0
28	TraesCS4B01G272800	chr1A	89.127	561	60	1	2335	2894	486809032	486808472	0.000000e+00	697.0
29	TraesCS4B01G272800	chr1A	79.292	367	40	18	843	1193	569356151	569355805	1.040000e-54	224.0
30	TraesCS4B01G272800	chr7D	94.397	464	25	1	2335	2797	125453050	125453513	0.000000e+00	712.0
31	TraesCS4B01G272800	chr6B	88.434	562	63	2	2335	2894	281634435	281633874	0.000000e+00	676.0
32	TraesCS4B01G272800	chr5A	86.121	562	76	2	2335	2894	604236176	604236737	3.190000e-169	604.0
33	TraesCS4B01G272800	chr7A	85.841	565	77	3	2332	2894	672879463	672880026	5.340000e-167	597.0

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	TraesCS4B01G272800	chr4B	550501807	550504701	2894	False	5347.000000	5347	100.0000	1	2895	1	chr4B.!!$F2	2894
1	TraesCS4B01G272800	chr4B	547309457	547310368	911	False	950.000000	950	85.5580	986	1894	1	chr4B.!!$F1	908
2	TraesCS4B01G272800	chr4B	550432062	550433909	1847	True	897.500000	1615	85.1115	1	2033	2	chr4B.!!$R1	2032
3	TraesCS4B01G272800	chr4B	550486646	550489237	2591	True	706.333333	1343	92.6230	221	2113	3	chr4B.!!$R2	1892
4	TraesCS4B01G272800	chr4D	442395158	442397187	2029	False	2900.000000	2900	92.5780	99	2120	1	chr4D.!!$F3	2021
5	TraesCS4B01G272800	chr4D	442221916	442224024	2108	True	1101.600000	2119	93.8805	222	2116	2	chr4D.!!$R2	1894
6	TraesCS4B01G272800	chr4D	441255867	441256779	912	False	935.000000	935	85.2460	986	1894	1	chr4D.!!$F1	908
7	TraesCS4B01G272800	chr4D	442214329	442216347	2018	True	925.500000	1666	84.6605	1	2033	2	chr4D.!!$R1	2032
8	TraesCS4B01G272800	chr4D	442247710	442251102	3392	True	703.733333	1930	86.3870	1	2120	3	chr4D.!!$R3	2119
9	TraesCS4B01G272800	chr4A	24935155	24936591	1436	False	1864.000000	1864	90.0410	576	2033	1	chr4A.!!$F1	1457
10	TraesCS4B01G272800	chr4A	24918262	24919987	1725	True	1160.500000	2211	91.5370	462	2237	2	chr4A.!!$R2	1775
11	TraesCS4B01G272800	chr4A	131993959	131994515	556	True	584.000000	584	85.7140	2339	2894	1	chr4A.!!$R1	555
12	TraesCS4B01G272800	chr5D	544798751	544799995	1244	False	952.000000	952	81.1230	657	1894	1	chr5D.!!$F1	1237
13	TraesCS4B01G272800	chr2B	96226853	96227413	560	True	902.000000	902	95.7220	2335	2894	1	chr2B.!!$R1	559
14	TraesCS4B01G272800	chr5B	687223392	687224630	1238	False	863.000000	863	79.8270	657	1894	1	chr5B.!!$F2	1237
15	TraesCS4B01G272800	chr5B	462728457	462729010	553	False	531.000000	531	83.9860	2321	2881	1	chr5B.!!$F1	560
16	TraesCS4B01G272800	chr1A	486759980	486760540	560	True	736.000000	736	90.3740	2335	2894	1	chr1A.!!$R1	559
17	TraesCS4B01G272800	chr1A	486808472	486809032	560	True	697.000000	697	89.1270	2335	2894	1	chr1A.!!$R2	559
18	TraesCS4B01G272800	chr6B	281633874	281634435	561	True	676.000000	676	88.4340	2335	2894	1	chr6B.!!$R1	559
19	TraesCS4B01G272800	chr5A	604236176	604236737	561	False	604.000000	604	86.1210	2335	2894	1	chr5A.!!$F1	559
20	TraesCS4B01G272800	chr7A	672879463	672880026	563	False	597.000000	597	85.8410	2332	2894	1	chr7A.!!$F1	562

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
260	1597	1.168714	GTTGGGCTTGCAGTTAGAGG	58.831	55.0	0.0	0.0	0.0	3.69	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1956	4482	0.038892	TTTACAGCGACACCTCGTCC	60.039	55.0	0.0	0.0	42.07	4.79	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
48	1134	8.714179	TGAAAAGAATAACCCGCATATAATACG	58.286	33.333	0.00	0.00	0.00	3.06
61	1147	8.182227	CCGCATATAATACGACTATTGAAGAGA	58.818	37.037	0.00	0.00	0.00	3.10
62	1148	9.216087	CGCATATAATACGACTATTGAAGAGAG	57.784	37.037	0.00	0.00	0.00	3.20
114	1200	7.577616	GCATGTTTTCTCTAAACCAATTAGGCT	60.578	37.037	0.00	0.00	44.49	4.58
146	1436	7.262772	CAAGTAATAATCAAGGTCGGTGTAGA	58.737	38.462	0.00	0.00	0.00	2.59
260	1597	1.168714	GTTGGGCTTGCAGTTAGAGG	58.831	55.000	0.00	0.00	0.00	3.69
306	1929	5.011635	AGCGGGAATTCCAAAGTAACAAAAT	59.988	36.000	25.67	0.00	37.91	1.82
317	1940	5.523438	AAGTAACAAAATTCCGGCTTTCA	57.477	34.783	0.00	0.00	0.00	2.69
344	1967	4.816385	TCAGCTACTTGTTCTTGTCTTTGG	59.184	41.667	0.00	0.00	0.00	3.28
380	2005	6.430000	GTCTGAATGTAGGTAGCCAAGAAAAA	59.570	38.462	0.00	0.00	0.00	1.94
421	2054	4.702612	TCTGGTGCGAAATGCCTTTAATTA	59.297	37.500	0.00	0.00	45.60	1.40
448	2082	1.954382	TGCATCTACTCGACGCCTTAT	59.046	47.619	0.00	0.00	27.50	1.73
494	2160	8.677300	TCTAATTAGCCAAGCAGAAAACATAAG	58.323	33.333	7.67	0.00	0.00	1.73
509	2176	8.495949	AGAAAACATAAGACATCACAAACGTAG	58.504	33.333	0.00	0.00	0.00	3.51
551	2218	6.173339	CAGTTCAGTATTAAAGGCCTCTTGA	58.827	40.000	5.23	0.00	32.75	3.02
591	2807	4.024809	ACTCAACAAAAGCGAGCTAGTTTC	60.025	41.667	0.00	0.00	0.00	2.78
711	2948	8.511748	AATTAAGGAAAGCTCTATAGATCCCA	57.488	34.615	14.09	3.27	0.00	4.37
712	2949	8.692682	ATTAAGGAAAGCTCTATAGATCCCAT	57.307	34.615	14.09	8.21	0.00	4.00
713	2950	9.790297	ATTAAGGAAAGCTCTATAGATCCCATA	57.210	33.333	14.09	7.46	0.00	2.74
714	2951	7.489239	AAGGAAAGCTCTATAGATCCCATAC	57.511	40.000	14.09	0.00	0.00	2.39
715	2952	5.654650	AGGAAAGCTCTATAGATCCCATACG	59.345	44.000	14.09	0.00	0.00	3.06
716	2953	5.419471	GGAAAGCTCTATAGATCCCATACGT	59.581	44.000	2.11	0.00	0.00	3.57
792	3050	3.453424	CATCCATACGATCGTTGGAACA	58.547	45.455	34.56	22.83	38.12	3.18
841	3101	4.208047	CACGACAATCATTTCTCTCGATCC	59.792	45.833	0.00	0.00	0.00	3.36
891	3171	2.443387	CACCATTGTCGCAATCATTCG	58.557	47.619	2.65	0.00	0.00	3.34

Showing 1 to 25 of 140 entries

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Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	6.177610	TGCGGGTTATTCTTTTCAGTTATCT	58.822	36.000	0.00	0.00	0.00	1.98
114	1200	6.819649	CGACCTTGATTATTACTTGGTAACCA	59.180	38.462	0.00	0.00	30.49	3.67
117	1203	6.819649	CACCGACCTTGATTATTACTTGGTAA	59.180	38.462	0.00	0.00	32.36	2.85
146	1436	4.402155	TGCTTCTTGTTCAAGGTCAAATGT	59.598	37.500	11.82	0.00	0.00	2.71
260	1597	4.830826	AGCCACAACTAACTAAAACTGC	57.169	40.909	0.00	0.00	0.00	4.40
306	1929	0.951558	GCTGAAAGTGAAAGCCGGAA	59.048	50.000	5.05	0.00	35.30	4.30
317	1940	5.675538	AGACAAGAACAAGTAGCTGAAAGT	58.324	37.500	0.00	0.00	35.30	2.66
344	1967	5.873164	ACCTACATTCAGACCGTACAATTTC	59.127	40.000	0.00	0.00	0.00	2.17
380	2005	3.952323	CCAGAGAAGATGCAACCATTCAT	59.048	43.478	0.00	0.00	0.00	2.57
421	2054	2.334838	GTCGAGTAGATGCAACCGTTT	58.665	47.619	0.00	0.00	0.00	3.60
494	2160	2.660236	GTCGACCTACGTTTGTGATGTC	59.340	50.000	3.51	0.00	43.13	3.06
509	2176	1.607148	CTGGTTTGAAAAGGGTCGACC	59.393	52.381	27.04	27.04	40.67	4.79
551	2218	2.098934	TGAGTGCGCACAAATGTTTCTT	59.901	40.909	39.21	17.06	0.00	2.52
591	2807	4.582701	AAGTCTATAGCAGTAGCAGCTG	57.417	45.455	10.11	10.11	45.49	4.24
654	2877	9.793252	CATTCAAAATGATAGGTTAACTGAAGG	57.207	33.333	5.42	2.59	0.00	3.46
709	2946	3.123804	GCAGGTCTGAATGTACGTATGG	58.876	50.000	0.00	0.00	0.00	2.74
710	2947	2.789339	CGCAGGTCTGAATGTACGTATG	59.211	50.000	0.00	0.00	0.00	2.39
711	2948	2.426024	ACGCAGGTCTGAATGTACGTAT	59.574	45.455	0.00	0.00	0.00	3.06
712	2949	1.814394	ACGCAGGTCTGAATGTACGTA	59.186	47.619	1.65	0.00	0.00	3.57
713	2950	0.601558	ACGCAGGTCTGAATGTACGT	59.398	50.000	1.65	0.00	0.00	3.57
714	2951	1.654105	GAACGCAGGTCTGAATGTACG	59.346	52.381	1.65	0.00	0.00	3.67
715	2952	2.683968	TGAACGCAGGTCTGAATGTAC	58.316	47.619	1.65	0.00	0.00	2.90
716	2953	3.394674	TTGAACGCAGGTCTGAATGTA	57.605	42.857	1.65	0.00	0.00	2.29
841	3101	9.979578	CTTAAATAGGATCTAGCTAGCATATGG	57.020	37.037	18.83	0.00	0.00	2.74
891	3171	2.675317	CGAGAGTGGATTTGGAGGTGAC	60.675	54.545	0.00	0.00	0.00	3.67

Showing 1 to 25 of 137 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.