AutoCloner

Multiple sequence alignment - TraesCS7A01G393000

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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	TraesCS7A01G393000	chr7A	100.000	2393	0	0	1	2393	570122387	570124779	0.000000e+00	4420.0
1	TraesCS7A01G393000	chr7A	91.930	285	13	4	859	1135	570141390	570141672	8.020000e-105	390.0
2	TraesCS7A01G393000	chr7A	81.953	338	33	17	300	635	570140789	570141100	6.560000e-66	261.0
3	TraesCS7A01G393000	chr7A	94.215	121	4	1	1126	1243	570143284	570143404	5.250000e-42	182.0
4	TraesCS7A01G393000	chr7A	85.380	171	13	5	688	858	570141106	570141264	1.470000e-37	167.0
5	TraesCS7A01G393000	chr7A	85.915	142	17	2	1911	2049	547552356	547552215	5.330000e-32	148.0
6	TraesCS7A01G393000	chr7D	92.741	2452	86	29	1	2393	502998660	503001078	0.000000e+00	3458.0
7	TraesCS7A01G393000	chr7D	92.165	970	59	6	440	1407	503686493	503687447	0.000000e+00	1354.0
8	TraesCS7A01G393000	chr7D	88.911	505	52	3	916	1419	503146269	503146770	9.400000e-174	619.0
9	TraesCS7A01G393000	chr7D	84.814	619	58	8	859	1476	503295998	503296581	7.370000e-165	590.0
10	TraesCS7A01G393000	chr7D	87.368	380	33	8	1220	1585	503039485	503039863	2.840000e-114	422.0
11	TraesCS7A01G393000	chr7D	88.112	286	20	9	242	527	503089113	503089384	6.380000e-86	327.0
12	TraesCS7A01G393000	chr7D	86.296	270	26	3	861	1130	503039007	503039265	1.400000e-72	283.0
13	TraesCS7A01G393000	chr7D	81.437	334	35	15	303	634	503295401	503295709	5.110000e-62	248.0
14	TraesCS7A01G393000	chr7D	87.209	172	9	5	688	859	503038737	503038895	1.460000e-42	183.0
15	TraesCS7A01G393000	chr7D	86.127	173	9	6	688	860	503295717	503295874	3.160000e-39	172.0
16	TraesCS7A01G393000	chr7D	92.105	114	8	1	528	641	503038624	503038736	2.460000e-35	159.0
17	TraesCS7A01G393000	chr7D	85.430	151	22	0	116	266	503295251	503295401	8.860000e-35	158.0
18	TraesCS7A01G393000	chr7D	79.167	240	21	12	303	540	503030922	503031134	3.210000e-29	139.0
19	TraesCS7A01G393000	chr7D	78.358	134	13	8	2274	2393	503700338	503700469	3.300000e-09	73.1
20	TraesCS7A01G393000	chr7D	89.655	58	3	2	2337	2393	503044433	503044488	1.190000e-08	71.3
21	TraesCS7A01G393000	chr7B	92.754	2208	93	24	107	2269	531664011	531666196	0.000000e+00	3129.0
22	TraesCS7A01G393000	chr7B	91.438	619	48	3	859	1476	531762594	531763208	0.000000e+00	845.0
23	TraesCS7A01G393000	chr7B	81.503	346	31	21	303	641	531761991	531762310	1.100000e-63	254.0
24	TraesCS7A01G393000	chr7B	81.223	229	37	5	1922	2147	328720880	328721105	1.890000e-41	180.0
25	TraesCS7A01G393000	chr7B	84.971	173	13	6	688	860	531762311	531762470	1.900000e-36	163.0
26	TraesCS7A01G393000	chr7B	80.000	250	24	19	1513	1742	531776916	531777159	6.850000e-36	161.0
27	TraesCS7A01G393000	chr7B	90.909	110	4	1	1	110	531663690	531663793	2.480000e-30	143.0
28	TraesCS7A01G393000	chr7B	91.667	96	5	2	2299	2393	531666198	531666291	1.930000e-26	130.0
29	TraesCS7A01G393000	chr3D	96.863	542	15	1	447	986	141837444	141836903	0.000000e+00	905.0
30	TraesCS7A01G393000	chr1A	80.159	252	44	4	1916	2163	336216130	336216379	1.460000e-42	183.0
31	TraesCS7A01G393000	chr1B	78.161	261	49	6	1916	2173	346406839	346407094	2.460000e-35	159.0
32	TraesCS7A01G393000	chr3B	76.000	225	43	9	1929	2147	737659903	737660122	3.250000e-19	106.0

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	TraesCS7A01G393000	chr7A	570122387	570124779	2392	False	4420.000000	4420	100.000000	1	2393	1	chr7A.!!$F1	2392
1	TraesCS7A01G393000	chr7A	570140789	570143404	2615	False	250.000000	390	88.369500	300	1243	4	chr7A.!!$F2	943
2	TraesCS7A01G393000	chr7D	502998660	503001078	2418	False	3458.000000	3458	92.741000	1	2393	1	chr7D.!!$F1	2392
3	TraesCS7A01G393000	chr7D	503686493	503687447	954	False	1354.000000	1354	92.165000	440	1407	1	chr7D.!!$F6	967
4	TraesCS7A01G393000	chr7D	503146269	503146770	501	False	619.000000	619	88.911000	916	1419	1	chr7D.!!$F5	503
5	TraesCS7A01G393000	chr7D	503295251	503296581	1330	False	292.000000	590	84.452000	116	1476	4	chr7D.!!$F9	1360
6	TraesCS7A01G393000	chr7D	503038624	503039863	1239	False	261.750000	422	88.244500	528	1585	4	chr7D.!!$F8	1057
7	TraesCS7A01G393000	chr7B	531663690	531666291	2601	False	1134.000000	3129	91.776667	1	2393	3	chr7B.!!$F3	2392
8	TraesCS7A01G393000	chr7B	531761991	531763208	1217	False	420.666667	845	85.970667	303	1476	3	chr7B.!!$F4	1173
9	TraesCS7A01G393000	chr3D	141836903	141837444	541	True	905.000000	905	96.863000	447	986	1	chr3D.!!$R1	539

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
55	56	2.034053	TGTTTTGGGTTCATTCAGCGAC	59.966	45.455	0.0	0.0	0.0	5.19	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1566	3744	0.110486	GGGAGCACACAGAAAAGGGA	59.89	55.0	0.0	0.0	0.0	4.2	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
52	53	3.451141	TGTGTTTTGGGTTCATTCAGC	57.549	42.857	0.00	0.00	0.00	4.26
55	56	2.034053	TGTTTTGGGTTCATTCAGCGAC	59.966	45.455	0.00	0.00	0.00	5.19
59	60	2.302260	TGGGTTCATTCAGCGACAAAA	58.698	42.857	0.00	0.00	0.00	2.44
60	61	2.890311	TGGGTTCATTCAGCGACAAAAT	59.110	40.909	0.00	0.00	0.00	1.82
138	360	2.380064	TGTTCACCTGGGCAAGAAAT	57.620	45.000	0.00	0.00	0.00	2.17
188	410	5.493809	TCAAGTTGTATACTTAGTTGGGGC	58.506	41.667	18.10	0.00	45.29	5.80
190	412	3.201487	AGTTGTATACTTAGTTGGGGCCC	59.799	47.826	18.17	18.17	31.29	5.80
249	477	6.607019	ACCAATGGAGTAAACCAGAAACTAA	58.393	36.000	6.16	0.00	43.49	2.24
267	495	7.706607	AGAAACTAATGTCAGCAAAAAGGTTTC	59.293	33.333	0.00	0.00	0.00	2.78
923	1291	9.203421	TGTTAGCGAAGTAATATGAACCATATG	57.797	33.333	0.00	0.00	37.17	1.78
1335	3500	0.323957	GCAGGGGGAAGAACTACGTT	59.676	55.000	0.00	0.00	0.00	3.99
1432	3597	4.150980	TGTTATTTGTCCGTGTTAGCTTCG	59.849	41.667	0.00	0.00	0.00	3.79
1483	3649	1.214367	TTTGTCGCGAAGTTCACTCC	58.786	50.000	12.06	0.00	0.00	3.85
1576	3754	3.336122	AGCAGTGCTCCCTTTTCTG	57.664	52.632	13.14	0.00	30.62	3.02
1577	3755	0.475906	AGCAGTGCTCCCTTTTCTGT	59.524	50.000	13.14	0.00	30.62	3.41
1578	3756	0.595095	GCAGTGCTCCCTTTTCTGTG	59.405	55.000	8.18	0.00	0.00	3.66
1579	3757	1.972872	CAGTGCTCCCTTTTCTGTGT	58.027	50.000	0.00	0.00	0.00	3.72
1588	3782	1.270625	CCTTTTCTGTGTGCTCCCGTA	60.271	52.381	0.00	0.00	0.00	4.02
1661	3855	4.962362	TCATAGCCATTCTTACTGGTGAGA	59.038	41.667	0.00	0.00	36.10	3.27
1674	3868	4.632153	ACTGGTGAGAATCTGTGTGTTAC	58.368	43.478	0.00	0.00	34.92	2.50
1868	4063	4.143030	CGTTCTTGATTTTCGCAGAGACAT	60.143	41.667	0.00	0.00	38.43	3.06
1895	4090	8.579006	GCATCAAATGGTATTTGGATCAGAATA	58.421	33.333	12.72	0.00	0.00	1.75
2109	4307	7.013942	ACCTGTTAAAACTTGGTAGGAATGAAC	59.986	37.037	8.58	0.00	35.73	3.18
2177	4409	4.080751	AGGGAATTGCAAGGAATCAAATGG	60.081	41.667	4.94	0.00	0.00	3.16
2178	4410	4.080975	GGGAATTGCAAGGAATCAAATGGA	60.081	41.667	4.94	0.00	0.00	3.41
2179	4411	5.490159	GGAATTGCAAGGAATCAAATGGAA	58.510	37.500	4.94	0.00	0.00	3.53
2180	4412	6.117488	GGAATTGCAAGGAATCAAATGGAAT	58.883	36.000	4.94	0.00	35.69	3.01
2181	4413	6.259387	GGAATTGCAAGGAATCAAATGGAATC	59.741	38.462	4.94	0.00	33.50	2.52
2182	4414	5.741962	TTGCAAGGAATCAAATGGAATCA	57.258	34.783	0.00	0.00	0.00	2.57
2183	4415	5.741962	TGCAAGGAATCAAATGGAATCAA	57.258	34.783	0.00	0.00	0.00	2.57
2184	4416	6.111669	TGCAAGGAATCAAATGGAATCAAA	57.888	33.333	0.00	0.00	0.00	2.69
2185	4417	6.713276	TGCAAGGAATCAAATGGAATCAAAT	58.287	32.000	0.00	0.00	0.00	2.32
2186	4418	6.596106	TGCAAGGAATCAAATGGAATCAAATG	59.404	34.615	0.00	0.00	0.00	2.32
2198	4430	4.220382	TGGAATCAAATGAGTTTGCGGATT	59.780	37.500	0.00	0.00	43.47	3.01
2280	4512	5.600069	GCCCTTGGGAATTTCTTATCAGAAT	59.400	40.000	10.36	0.00	38.89	2.40
2297	4529	0.108585	AATGAGGTGTCGTTGTGCCT	59.891	50.000	0.00	0.00	30.21	4.75
2336	4568	4.202357	TGCGGAATCTATATGGAGCTTTGT	60.202	41.667	0.00	0.00	0.00	2.83

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
52	53	3.543670	GCCATTTGCACAAATTTTGTCG	58.456	40.909	11.78	9.00	43.23	4.35
138	360	6.404293	GCAAACAGGTTTAAGAAACACTGAGA	60.404	38.462	18.90	0.00	43.15	3.27
188	410	0.607489	CACTGAAGGTCAAGGCTGGG	60.607	60.000	0.00	0.00	0.00	4.45
190	412	0.250640	AGCACTGAAGGTCAAGGCTG	60.251	55.000	0.00	0.00	35.42	4.85
249	477	5.105392	TGACTTGAAACCTTTTTGCTGACAT	60.105	36.000	0.00	0.00	0.00	3.06
267	495	5.066375	TGTTTGAGGACAGAAACATGACTTG	59.934	40.000	0.00	0.00	31.06	3.16
950	1321	3.933332	CGTTAAAAGAGACCCTGACCATC	59.067	47.826	0.00	0.00	0.00	3.51
1335	3500	2.038007	AGCCGCTTCTCCTCCTCA	59.962	61.111	0.00	0.00	0.00	3.86
1483	3649	4.627467	GTGATACAGAATAAGCATAGCCCG	59.373	45.833	0.00	0.00	0.00	6.13
1564	3742	0.877743	GAGCACACAGAAAAGGGAGC	59.122	55.000	0.00	0.00	0.00	4.70
1565	3743	1.528129	GGAGCACACAGAAAAGGGAG	58.472	55.000	0.00	0.00	0.00	4.30
1566	3744	0.110486	GGGAGCACACAGAAAAGGGA	59.890	55.000	0.00	0.00	0.00	4.20
1567	3745	1.237285	CGGGAGCACACAGAAAAGGG	61.237	60.000	0.00	0.00	0.00	3.95
1568	3746	0.535102	ACGGGAGCACACAGAAAAGG	60.535	55.000	0.00	0.00	0.00	3.11
1569	3747	2.163818	TACGGGAGCACACAGAAAAG	57.836	50.000	0.00	0.00	0.00	2.27
1570	3748	2.614481	GGATACGGGAGCACACAGAAAA	60.614	50.000	0.00	0.00	0.00	2.29
1571	3749	1.066430	GGATACGGGAGCACACAGAAA	60.066	52.381	0.00	0.00	0.00	2.52
1572	3750	0.535335	GGATACGGGAGCACACAGAA	59.465	55.000	0.00	0.00	0.00	3.02
1573	3751	0.613572	TGGATACGGGAGCACACAGA	60.614	55.000	0.00	0.00	42.51	3.41
1574	3752	0.465705	ATGGATACGGGAGCACACAG	59.534	55.000	0.00	0.00	42.51	3.66
1575	3753	0.464036	GATGGATACGGGAGCACACA	59.536	55.000	0.00	0.00	42.51	3.72
1576	3754	0.753262	AGATGGATACGGGAGCACAC	59.247	55.000	0.00	0.00	42.51	3.82
1577	3755	1.412710	GAAGATGGATACGGGAGCACA	59.587	52.381	0.00	0.00	42.51	4.57
1578	3756	1.603172	CGAAGATGGATACGGGAGCAC	60.603	57.143	0.00	0.00	42.51	4.40
1579	3757	0.673985	CGAAGATGGATACGGGAGCA	59.326	55.000	0.00	0.00	42.51	4.26
1588	3782	5.304101	GGATCTATCATAGCCGAAGATGGAT	59.696	44.000	0.00	0.00	40.99	3.41
1661	3855	3.807622	CACTTCACCGTAACACACAGATT	59.192	43.478	0.00	0.00	0.00	2.40
1703	3897	1.464734	TAGTCAGCCTTCCGAGACAG	58.535	55.000	0.00	0.00	33.56	3.51
1868	4063	5.892686	TCTGATCCAAATACCATTTGATGCA	59.107	36.000	12.13	0.00	0.00	3.96
1895	4090	0.322546	GGTCACAAATCGCCTCCCTT	60.323	55.000	0.00	0.00	0.00	3.95
2144	4342	4.039124	CCTTGCAATTCCCTGTACAGTTTT	59.961	41.667	21.18	6.58	0.00	2.43
2152	4350	3.173953	TGATTCCTTGCAATTCCCTGT	57.826	42.857	0.00	0.00	0.00	4.00
2153	4351	4.540359	TTTGATTCCTTGCAATTCCCTG	57.460	40.909	0.00	0.00	0.00	4.45
2181	4413	2.988493	CCACAATCCGCAAACTCATTTG	59.012	45.455	0.00	0.00	46.81	2.32
2182	4414	2.029110	CCCACAATCCGCAAACTCATTT	60.029	45.455	0.00	0.00	0.00	2.32
2183	4415	1.545582	CCCACAATCCGCAAACTCATT	59.454	47.619	0.00	0.00	0.00	2.57
2184	4416	1.176527	CCCACAATCCGCAAACTCAT	58.823	50.000	0.00	0.00	0.00	2.90
2185	4417	0.893270	CCCCACAATCCGCAAACTCA	60.893	55.000	0.00	0.00	0.00	3.41
2186	4418	1.883021	CCCCACAATCCGCAAACTC	59.117	57.895	0.00	0.00	0.00	3.01
2198	4430	4.738998	CGGGAGCATTGCCCCACA	62.739	66.667	25.52	0.00	42.92	4.17
2280	4512	1.069090	GAGGCACAACGACACCTCA	59.931	57.895	3.07	0.00	46.57	3.86
2297	4529	1.452110	CGCAGATTGTTCCCATGTGA	58.548	50.000	0.00	0.00	0.00	3.58
2336	4568	5.733655	GCGAAGGTAGAAGAGATTGATCGAA	60.734	44.000	0.00	0.00	0.00	3.71
2367	4599	8.839310	GAAAATAGCAGCAGGAGATTAGAATA	57.161	34.615	0.00	0.00	0.00	1.75

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.