AutoCloner

Multiple sequence alignment - TraesCS5B01G453500

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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	TraesCS5B01G453500	chr5B	100.000	2543	0	0	1	2543	626194128	626191586	0.000000e+00	4697
1	TraesCS5B01G453500	chr5B	83.706	1209	160	24	1142	2323	626090688	626089490	0.000000e+00	1107
2	TraesCS5B01G453500	chr5B	86.835	714	82	9	1620	2323	631359301	631358590	0.000000e+00	787
3	TraesCS5B01G453500	chr5B	83.108	592	93	6	812	1401	631365992	631365406	1.340000e-147	532
4	TraesCS5B01G453500	chr5B	81.241	709	59	26	97	773	631366661	631365995	2.920000e-139	505
5	TraesCS5B01G453500	chr5B	78.884	502	80	18	1832	2323	626083538	626083053	1.470000e-82	316
6	TraesCS5B01G453500	chr5B	87.425	167	16	3	2379	2541	626089001	626088836	1.200000e-43	187
7	TraesCS5B01G453500	chr5B	86.145	166	19	4	2379	2541	631358064	631357900	2.600000e-40	176
8	TraesCS5B01G453500	chr5B	81.250	208	14	9	355	558	626140993	626140807	7.330000e-31	145
9	TraesCS5B01G453500	chr5B	77.947	263	26	13	300	558	626085341	626085107	4.410000e-28	135
10	TraesCS5B01G453500	chr5B	76.779	267	33	13	295	558	626107390	626107150	3.440000e-24	122
11	TraesCS5B01G453500	chr5B	76.806	263	29	14	300	558	631379089	631378855	4.440000e-23	119
12	TraesCS5B01G453500	chr5B	91.566	83	7	0	476	558	631354465	631354383	5.750000e-22	115
13	TraesCS5B01G453500	chr5D	95.181	1328	53	3	1007	2323	502545279	502543952	0.000000e+00	2087
14	TraesCS5B01G453500	chr5D	91.168	1053	52	15	1	1039	502546227	502545202	0.000000e+00	1391
15	TraesCS5B01G453500	chr5D	82.209	1349	199	30	1002	2323	502377083	502375749	0.000000e+00	1123
16	TraesCS5B01G453500	chr5D	96.983	232	6	1	2312	2543	502543566	502543336	3.070000e-104	388
17	TraesCS5B01G453500	chr5D	87.805	164	18	2	2379	2541	502375260	502375098	9.290000e-45	191
18	TraesCS5B01G453500	chr5D	80.769	208	15	9	355	558	502537462	502537276	3.410000e-29	139
19	TraesCS5B01G453500	chr5D	93.976	83	5	0	476	558	502365146	502365064	2.660000e-25	126
20	TraesCS5B01G453500	chr5A	82.715	1348	202	20	997	2323	631230855	631229518	0.000000e+00	1170
21	TraesCS5B01G453500	chr5A	91.582	784	20	16	1	778	631261006	631260263	0.000000e+00	1040
22	TraesCS5B01G453500	chr5A	82.423	1172	185	16	1088	2243	631206513	631205347	0.000000e+00	1003
23	TraesCS5B01G453500	chr5A	82.984	764	119	9	943	1701	631259882	631259125	0.000000e+00	680
24	TraesCS5B01G453500	chr5A	77.855	429	80	13	1902	2323	631083456	631083036	4.200000e-63	252
25	TraesCS5B01G453500	chr5A	92.793	111	8	0	821	931	631260252	631260142	7.280000e-36	161

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	TraesCS5B01G453500	chr5B	626191586	626194128	2542	True	4697.000000	4697	100.000000	1	2543	1	chr5B.!!$R3	2542
1	TraesCS5B01G453500	chr5B	631365406	631366661	1255	True	518.500000	532	82.174500	97	1401	2	chr5B.!!$R7	1304
2	TraesCS5B01G453500	chr5B	626083053	626090688	7635	True	436.250000	1107	81.990500	300	2541	4	chr5B.!!$R5	2241
3	TraesCS5B01G453500	chr5B	631354383	631359301	4918	True	359.333333	787	88.182000	476	2541	3	chr5B.!!$R6	2065
4	TraesCS5B01G453500	chr5D	502543336	502546227	2891	True	1288.666667	2087	94.444000	1	2543	3	chr5D.!!$R4	2542
5	TraesCS5B01G453500	chr5D	502375098	502377083	1985	True	657.000000	1123	85.007000	1002	2541	2	chr5D.!!$R3	1539
6	TraesCS5B01G453500	chr5A	631229518	631230855	1337	True	1170.000000	1170	82.715000	997	2323	1	chr5A.!!$R3	1326
7	TraesCS5B01G453500	chr5A	631205347	631206513	1166	True	1003.000000	1003	82.423000	1088	2243	1	chr5A.!!$R2	1155
8	TraesCS5B01G453500	chr5A	631259125	631261006	1881	True	627.000000	1040	89.119667	1	1701	3	chr5A.!!$R4	1700

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
860	902	0.110688	CGATGCGGGCAATGAATACG	60.111	55.0	0.0	0.0	0.0	3.06	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1965	2322	0.320374	TGTCTAAAGCCACTGTCCCG	59.68	55.0	0.0	0.0	0.0	5.14	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
64	65	2.815211	TGCGCGAACAGCTCCATC	60.815	61.111	12.10	0.00	45.59	3.51
112	114	2.032071	GACGGTGGTTGTCTGGGG	59.968	66.667	0.00	0.00	33.54	4.96
128	130	3.341833	GGGGGAATTCTCTCTGGGA	57.658	57.895	5.06	0.00	0.00	4.37
129	131	1.826447	GGGGGAATTCTCTCTGGGAT	58.174	55.000	5.06	0.00	0.00	3.85
130	132	1.423161	GGGGGAATTCTCTCTGGGATG	59.577	57.143	5.06	0.00	0.00	3.51
131	133	1.423161	GGGGAATTCTCTCTGGGATGG	59.577	57.143	5.06	0.00	0.00	3.51
132	134	2.412591	GGGAATTCTCTCTGGGATGGA	58.587	52.381	5.23	0.00	0.00	3.41
138	140	1.862242	TCTCTCTGGGATGGAGGATGA	59.138	52.381	0.00	0.00	0.00	2.92
283	285	2.203640	TCTGTCGGTGAGGGCAGT	60.204	61.111	0.00	0.00	0.00	4.40
289	291	1.528309	CGGTGAGGGCAGTGGTTTT	60.528	57.895	0.00	0.00	0.00	2.43
470	503	3.994853	GTTTCCGTCCCGTCCCGT	61.995	66.667	0.00	0.00	0.00	5.28
493	526	0.787183	GCTGCGAGACTGAAACTGAC	59.213	55.000	0.00	0.00	0.00	3.51
561	602	2.489329	GGATGGACGGATGCCAATAATG	59.511	50.000	0.00	0.00	39.21	1.90
818	860	1.504359	AAGAAAAACCGCGTCGATCA	58.496	45.000	4.92	0.00	0.00	2.92
819	861	1.722011	AGAAAAACCGCGTCGATCAT	58.278	45.000	4.92	0.00	0.00	2.45
860	902	0.110688	CGATGCGGGCAATGAATACG	60.111	55.000	0.00	0.00	0.00	3.06
900	942	1.320344	AATCTAGACGCGGAGGCACA	61.320	55.000	12.47	0.00	39.92	4.57
953	1243	1.946768	CCGACCTCTGTCTCAGATCTC	59.053	57.143	0.00	0.00	39.92	2.75
954	1244	2.637947	CGACCTCTGTCTCAGATCTCA	58.362	52.381	0.00	0.00	39.92	3.27
955	1245	3.013219	CGACCTCTGTCTCAGATCTCAA	58.987	50.000	0.00	0.00	39.92	3.02
956	1246	3.181501	CGACCTCTGTCTCAGATCTCAAC	60.182	52.174	0.00	0.00	39.92	3.18
957	1247	3.761218	GACCTCTGTCTCAGATCTCAACA	59.239	47.826	0.00	0.00	39.92	3.33
958	1248	4.155709	ACCTCTGTCTCAGATCTCAACAA	58.844	43.478	0.00	0.00	39.92	2.83
959	1249	4.021544	ACCTCTGTCTCAGATCTCAACAAC	60.022	45.833	0.00	0.00	39.92	3.32
960	1250	4.021632	CCTCTGTCTCAGATCTCAACAACA	60.022	45.833	0.00	0.00	39.92	3.33
961	1251	5.510349	CCTCTGTCTCAGATCTCAACAACAA	60.510	44.000	0.00	0.00	39.92	2.83
962	1252	5.917462	TCTGTCTCAGATCTCAACAACAAA	58.083	37.500	0.00	0.00	35.39	2.83
963	1253	6.348498	TCTGTCTCAGATCTCAACAACAAAA	58.652	36.000	0.00	0.00	35.39	2.44
964	1254	6.481313	TCTGTCTCAGATCTCAACAACAAAAG	59.519	38.462	0.00	0.00	35.39	2.27
965	1255	5.528690	TGTCTCAGATCTCAACAACAAAAGG	59.471	40.000	0.00	0.00	0.00	3.11
966	1256	5.049129	GTCTCAGATCTCAACAACAAAAGGG	60.049	44.000	0.00	0.00	0.00	3.95
967	1257	3.569701	TCAGATCTCAACAACAAAAGGGC	59.430	43.478	0.00	0.00	0.00	5.19
968	1258	2.893489	AGATCTCAACAACAAAAGGGCC	59.107	45.455	0.00	0.00	0.00	5.80
969	1259	2.452600	TCTCAACAACAAAAGGGCCT	57.547	45.000	0.00	0.00	0.00	5.19
970	1260	2.745968	TCTCAACAACAAAAGGGCCTT	58.254	42.857	14.48	14.48	0.00	4.35
971	1261	2.430332	TCTCAACAACAAAAGGGCCTTG	59.570	45.455	21.72	12.05	0.00	3.61
972	1262	1.484240	TCAACAACAAAAGGGCCTTGG	59.516	47.619	21.72	17.57	0.00	3.61
973	1263	0.836606	AACAACAAAAGGGCCTTGGG	59.163	50.000	21.72	17.19	0.00	4.12
1153	1485	1.277842	ACATGTGGTACAAGGATGCGA	59.722	47.619	0.00	0.00	44.16	5.10
1173	1505	1.727062	AGGAGATGCATCGGGATTCT	58.273	50.000	20.67	4.85	0.00	2.40
1209	1541	2.443255	AGAGGCTTTGAAGGAGGAACAA	59.557	45.455	0.00	0.00	0.00	2.83
1215	1547	5.279657	GGCTTTGAAGGAGGAACAAATTCAT	60.280	40.000	0.00	0.00	36.46	2.57
1326	1661	0.452122	CGTCACGCGATTGGGTTTTC	60.452	55.000	15.93	0.00	44.77	2.29
1331	1666	1.136774	GCGATTGGGTTTTCTCCGC	59.863	57.895	0.00	0.00	0.00	5.54
1539	1877	2.099638	CGGAGCGTCGACGATGAA	59.900	61.111	39.74	0.00	43.02	2.57
1702	2046	1.271926	GGTGTGGGGATTTGTAGCTGT	60.272	52.381	0.00	0.00	0.00	4.40
1789	2133	2.424557	AGATGATCATGCCGCTGATTC	58.575	47.619	14.30	0.00	36.01	2.52
1855	2199	2.953284	CATCAGAAGGGGATGATGCT	57.047	50.000	2.55	0.00	44.43	3.79
1896	2242	0.538516	CCATCCCGGTTGGTGTGAAA	60.539	55.000	11.63	0.00	34.77	2.69
1984	2341	0.320374	CGGGACAGTGGCTTTAGACA	59.680	55.000	0.00	0.00	0.00	3.41
2034	2392	2.655090	TCTTGGCCTCATGAACACAA	57.345	45.000	3.32	1.36	0.00	3.33
2042	2400	4.941263	GGCCTCATGAACACAACTATGTTA	59.059	41.667	0.00	0.00	42.89	2.41
2043	2401	5.414454	GGCCTCATGAACACAACTATGTTAA	59.586	40.000	0.00	0.00	42.89	2.01
2175	2534	5.238583	ACTCCCATTTTTAGTTGAGTCTCG	58.761	41.667	0.00	0.00	0.00	4.04
2538	3378	2.238084	AAGGAGGGAAATCAAAGGGC	57.762	50.000	0.00	0.00	0.00	5.19

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
112	114	2.371510	CTCCATCCCAGAGAGAATTCCC	59.628	54.545	0.65	0.00	32.86	3.97
126	128	0.539051	CCGCCTATCATCCTCCATCC	59.461	60.000	0.00	0.00	0.00	3.51
127	129	0.107945	GCCGCCTATCATCCTCCATC	60.108	60.000	0.00	0.00	0.00	3.51
128	130	1.892819	CGCCGCCTATCATCCTCCAT	61.893	60.000	0.00	0.00	0.00	3.41
129	131	2.574018	CGCCGCCTATCATCCTCCA	61.574	63.158	0.00	0.00	0.00	3.86
130	132	2.219325	CTCGCCGCCTATCATCCTCC	62.219	65.000	0.00	0.00	0.00	4.30
131	133	1.214062	CTCGCCGCCTATCATCCTC	59.786	63.158	0.00	0.00	0.00	3.71
132	134	2.279069	CCTCGCCGCCTATCATCCT	61.279	63.158	0.00	0.00	0.00	3.24
138	140	2.499685	GTCAACCTCGCCGCCTAT	59.500	61.111	0.00	0.00	0.00	2.57
171	173	1.818674	ACCAAAATCAATCACCTCGCC	59.181	47.619	0.00	0.00	0.00	5.54
172	174	3.244976	CAACCAAAATCAATCACCTCGC	58.755	45.455	0.00	0.00	0.00	5.03
173	175	4.229096	CACAACCAAAATCAATCACCTCG	58.771	43.478	0.00	0.00	0.00	4.63
174	176	4.559153	CCACAACCAAAATCAATCACCTC	58.441	43.478	0.00	0.00	0.00	3.85
175	177	3.244181	GCCACAACCAAAATCAATCACCT	60.244	43.478	0.00	0.00	0.00	4.00
283	285	1.205893	GGTCAAACCAGCACAAAACCA	59.794	47.619	0.00	0.00	38.42	3.67
289	291	1.077357	AACGGGTCAAACCAGCACA	60.077	52.632	0.00	0.00	41.02	4.57
470	503	2.570284	TTTCAGTCTCGCAGCGGGA	61.570	57.895	15.10	15.10	32.29	5.14
472	505	1.373497	AGTTTCAGTCTCGCAGCGG	60.373	57.895	16.42	5.91	0.00	5.52
473	506	0.664466	TCAGTTTCAGTCTCGCAGCG	60.664	55.000	9.06	9.06	0.00	5.18
493	526	3.636043	ACCAAACGTGACGCTGCG	61.636	61.111	21.91	21.91	0.00	5.18
561	602	8.463607	AGCAACTGAGAGAGAAGTATACTAAAC	58.536	37.037	5.65	1.45	0.00	2.01
580	621	7.871853	ACTAATACTTAAACACCAAGCAACTG	58.128	34.615	0.00	0.00	0.00	3.16
785	827	7.411480	CGCGGTTTTTCTTTCTTTCTTTCTTTT	60.411	33.333	0.00	0.00	0.00	2.27
818	860	0.331278	TTTCCCCGAGATTGGTGCAT	59.669	50.000	0.00	0.00	0.00	3.96
819	861	0.608035	GTTTCCCCGAGATTGGTGCA	60.608	55.000	0.00	0.00	0.00	4.57
860	902	2.989422	AATGCCTGCAAAAGTCGTAC	57.011	45.000	0.00	0.00	0.00	3.67
900	942	2.599677	GGATGGATCGTAGAGACCCTT	58.400	52.381	0.00	0.00	43.63	3.95
953	1243	1.474855	CCCAAGGCCCTTTTGTTGTTG	60.475	52.381	0.00	0.00	0.00	3.33
954	1244	0.836606	CCCAAGGCCCTTTTGTTGTT	59.163	50.000	0.00	0.00	0.00	2.83
955	1245	1.695114	GCCCAAGGCCCTTTTGTTGT	61.695	55.000	0.00	0.00	44.06	3.32
956	1246	1.071299	GCCCAAGGCCCTTTTGTTG	59.929	57.895	0.00	0.00	44.06	3.33
957	1247	3.562250	GCCCAAGGCCCTTTTGTT	58.438	55.556	0.00	0.00	44.06	2.83
1153	1485	2.038295	GAGAATCCCGATGCATCTCCTT	59.962	50.000	23.73	11.80	32.30	3.36
1173	1505	1.667154	CCTCTCGAATCACCAGGCGA	61.667	60.000	0.00	0.00	0.00	5.54
1539	1877	1.759562	GCTAGCCAGGGAGACACCTAT	60.760	57.143	2.29	0.00	39.34	2.57
1576	1914	3.391382	CGGACTCCTTCCCGGCTT	61.391	66.667	0.00	0.00	42.27	4.35
1702	2046	5.185056	TCACATCTCTGAACCGTATTTCTCA	59.815	40.000	0.00	0.00	0.00	3.27
1896	2242	5.156608	CCATGAAGAAATTGGCTCCTTTT	57.843	39.130	0.00	0.00	0.00	2.27
1965	2322	0.320374	TGTCTAAAGCCACTGTCCCG	59.680	55.000	0.00	0.00	0.00	5.14
1984	2341	0.624500	TAGGCCCCCTTGCTCTTCAT	60.625	55.000	0.00	0.00	34.61	2.57
2042	2400	8.697292	GTCTCTAACTTCCATAACCATCTAGTT	58.303	37.037	0.00	0.00	0.00	2.24
2043	2401	8.062536	AGTCTCTAACTTCCATAACCATCTAGT	58.937	37.037	0.00	0.00	33.03	2.57
2356	3155	5.924475	AGACCAACTAAATGACAAACTCG	57.076	39.130	0.00	0.00	0.00	4.18
2365	3164	5.473504	AGCACCAACTAAGACCAACTAAATG	59.526	40.000	0.00	0.00	0.00	2.32

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.