AutoCloner

Multiple sequence alignment - TraesCS2A01G519100

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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	TraesCS2A01G519100	chr2A	100.000	2339	0	0	1	2339	742309307	742306969	0.000000e+00	4320
1	TraesCS2A01G519100	chr2A	88.299	735	69	9	1613	2339	744634407	744633682	0.000000e+00	865
2	TraesCS2A01G519100	chr2A	89.017	173	12	5	1367	1532	744634722	744634550	8.470000e-50	207
3	TraesCS2A01G519100	chr7D	96.994	1364	38	3	1	1363	232924947	232926308	0.000000e+00	2289
4	TraesCS2A01G519100	chr7D	96.706	1366	41	4	1	1364	149106978	149105615	0.000000e+00	2270
5	TraesCS2A01G519100	chr7D	96.413	1366	45	4	1	1364	497912483	497911120	0.000000e+00	2248
6	TraesCS2A01G519100	chr2D	96.852	1366	38	5	1	1363	273017911	273019274	0.000000e+00	2279
7	TraesCS2A01G519100	chr2D	93.810	727	35	7	1614	2339	609637923	609638640	0.000000e+00	1085
8	TraesCS2A01G519100	chr2D	88.995	736	64	11	1613	2339	612696189	612695462	0.000000e+00	894
9	TraesCS2A01G519100	chr2D	87.602	734	66	12	1614	2339	612977980	612977264	0.000000e+00	828
10	TraesCS2A01G519100	chr2D	87.318	481	44	9	1613	2086	612758223	612757753	3.420000e-148	534
11	TraesCS2A01G519100	chr2D	93.567	171	8	3	1367	1535	609637415	609637584	3.860000e-63	252
12	TraesCS2A01G519100	chr2D	92.814	167	12	0	2173	2339	612754211	612754045	2.320000e-60	243
13	TraesCS2A01G519100	chr2D	86.047	172	18	4	1367	1532	612758581	612758410	1.850000e-41	180
14	TraesCS2A01G519100	chr2D	92.000	75	6	0	1541	1615	609637761	609637835	3.180000e-19	106
15	TraesCS2A01G519100	chr5A	96.557	1365	42	5	1	1363	635794533	635793172	0.000000e+00	2255
16	TraesCS2A01G519100	chr3D	96.337	1365	45	5	1	1363	87390036	87391397	0.000000e+00	2239
17	TraesCS2A01G519100	chr6A	95.827	1366	47	9	1	1363	35542452	35543810	0.000000e+00	2198
18	TraesCS2A01G519100	chr6A	92.826	1366	92	5	1	1363	371337482	371338844	0.000000e+00	1975
19	TraesCS2A01G519100	chr1B	92.742	1364	94	4	1	1362	611789588	611790948	0.000000e+00	1965
20	TraesCS2A01G519100	chr2B	88.179	736	57	11	1613	2339	747781965	747781251	0.000000e+00	850
21	TraesCS2A01G519100	chr2B	86.575	730	66	10	1613	2338	747853573	747852872	0.000000e+00	776
22	TraesCS2A01G519100	chr2B	86.172	687	59	17	1666	2339	747787685	747787022	0.000000e+00	710
23	TraesCS2A01G519100	chr2B	78.545	275	30	15	1369	1615	747853933	747853660	1.120000e-33	154

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	TraesCS2A01G519100	chr2A	742306969	742309307	2338	True	4320	4320	100.000000	1	2339	1	chr2A.!!$R1	2338
1	TraesCS2A01G519100	chr2A	744633682	744634722	1040	True	536	865	88.658000	1367	2339	2	chr2A.!!$R2	972
2	TraesCS2A01G519100	chr7D	232924947	232926308	1361	False	2289	2289	96.994000	1	1363	1	chr7D.!!$F1	1362
3	TraesCS2A01G519100	chr7D	149105615	149106978	1363	True	2270	2270	96.706000	1	1364	1	chr7D.!!$R1	1363
4	TraesCS2A01G519100	chr7D	497911120	497912483	1363	True	2248	2248	96.413000	1	1364	1	chr7D.!!$R2	1363
5	TraesCS2A01G519100	chr2D	273017911	273019274	1363	False	2279	2279	96.852000	1	1363	1	chr2D.!!$F1	1362
6	TraesCS2A01G519100	chr2D	612695462	612696189	727	True	894	894	88.995000	1613	2339	1	chr2D.!!$R1	726
7	TraesCS2A01G519100	chr2D	612977264	612977980	716	True	828	828	87.602000	1614	2339	1	chr2D.!!$R2	725
8	TraesCS2A01G519100	chr2D	609637415	609638640	1225	False	481	1085	93.125667	1367	2339	3	chr2D.!!$F2	972
9	TraesCS2A01G519100	chr2D	612754045	612758581	4536	True	319	534	88.726333	1367	2339	3	chr2D.!!$R3	972
10	TraesCS2A01G519100	chr5A	635793172	635794533	1361	True	2255	2255	96.557000	1	1363	1	chr5A.!!$R1	1362
11	TraesCS2A01G519100	chr3D	87390036	87391397	1361	False	2239	2239	96.337000	1	1363	1	chr3D.!!$F1	1362
12	TraesCS2A01G519100	chr6A	35542452	35543810	1358	False	2198	2198	95.827000	1	1363	1	chr6A.!!$F1	1362
13	TraesCS2A01G519100	chr6A	371337482	371338844	1362	False	1975	1975	92.826000	1	1363	1	chr6A.!!$F2	1362
14	TraesCS2A01G519100	chr1B	611789588	611790948	1360	False	1965	1965	92.742000	1	1362	1	chr1B.!!$F1	1361
15	TraesCS2A01G519100	chr2B	747781251	747781965	714	True	850	850	88.179000	1613	2339	1	chr2B.!!$R1	726
16	TraesCS2A01G519100	chr2B	747787022	747787685	663	True	710	710	86.172000	1666	2339	1	chr2B.!!$R2	673
17	TraesCS2A01G519100	chr2B	747852872	747853933	1061	True	465	776	82.560000	1369	2338	2	chr2B.!!$R3	969

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
918	925	1.492176	CCATGACTTGCTGGAGGGTAT	59.508	52.381	0.0	0.0	34.24	2.73	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1769	2056	3.006967	TCTTCAGCTGTGGAGACTTTACC	59.993	47.826	14.67	0.0	32.82	2.85	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
177	180	2.691409	ACTATGTGGACCATTGACGG	57.309	50.000	0.00	0.00	34.86	4.79
384	387	7.168302	GTGTCAGATATGGAAGTTATCTTGTCG	59.832	40.741	0.00	0.00	34.85	4.35
582	587	7.018550	AGGCTAGGGTTGGATATGATTATTGAA	59.981	37.037	0.00	0.00	0.00	2.69
759	764	5.521372	GCATAAGGAATTCACTCAAAATGCC	59.479	40.000	7.93	0.00	32.59	4.40
918	925	1.492176	CCATGACTTGCTGGAGGGTAT	59.508	52.381	0.00	0.00	34.24	2.73
958	967	7.177216	TGAGAGACGACAAAGGTAGGTTTATTA	59.823	37.037	0.00	0.00	0.00	0.98
975	984	6.666113	GGTTTATTACAGGAGGGAATGGAAAA	59.334	38.462	0.00	0.00	0.00	2.29
984	993	7.129504	ACAGGAGGGAATGGAAAAATAGACTAT	59.870	37.037	0.00	0.00	0.00	2.12
1079	1088	3.459232	TCGCCTAATCATCAACTCTGG	57.541	47.619	0.00	0.00	0.00	3.86
1096	1105	1.281867	CTGGCAATCTGGAGGTGGTTA	59.718	52.381	0.00	0.00	0.00	2.85
1184	1193	9.346005	TCACTATGCTTGTGATTTTATCATGAT	57.654	29.630	13.81	13.81	42.04	2.45
1284	1293	3.017442	GGTTTGGTTTGAGGAGCCTATC	58.983	50.000	0.00	0.00	0.00	2.08
1390	1399	1.153208	CCTGGAGCTAGCTTGCTGG	60.153	63.158	27.38	17.77	44.17	4.85
1397	1406	0.394899	GCTAGCTTGCTGGGTTGGAT	60.395	55.000	13.17	0.00	0.00	3.41
1532	1553	4.811555	TCGTTTTGACATCTGAAGTTGG	57.188	40.909	0.00	0.00	0.00	3.77
1533	1554	4.447290	TCGTTTTGACATCTGAAGTTGGA	58.553	39.130	0.00	0.00	0.00	3.53
1534	1555	4.878971	TCGTTTTGACATCTGAAGTTGGAA	59.121	37.500	0.00	0.00	0.00	3.53
1537	1558	6.697019	CGTTTTGACATCTGAAGTTGGAAAAT	59.303	34.615	0.00	0.00	0.00	1.82
1538	1559	7.096477	CGTTTTGACATCTGAAGTTGGAAAATC	60.096	37.037	0.00	0.00	0.00	2.17
1551	1745	7.018635	AGTTGGAAAATCGTTTCTTTCGTTA	57.981	32.000	0.00	0.00	42.45	3.18
1572	1766	6.965500	CGTTAGTCAGATACACGAATTACTGT	59.035	38.462	0.00	0.00	0.00	3.55
1578	1772	5.004440	CAGATACACGAATTACTGTGGAACG	59.996	44.000	9.09	0.00	42.39	3.95
1618	1901	1.738099	CTTCTGTTCCGCTGACCCG	60.738	63.158	0.00	0.00	0.00	5.28
1755	2042	4.065088	GCAGTCTTCACATGAACACCTTA	58.935	43.478	0.00	0.00	0.00	2.69
1819	2106	0.098728	GCACACGCACAACTTCAGTT	59.901	50.000	0.00	0.00	37.05	3.16
1948	2271	1.698506	AATTTGTTTCTGACGGGCCA	58.301	45.000	4.39	0.00	0.00	5.36
1955	2279	2.124983	CTGACGGGCCATGTGAGG	60.125	66.667	4.39	0.00	0.00	3.86
1956	2280	2.927856	TGACGGGCCATGTGAGGT	60.928	61.111	4.39	0.00	0.00	3.85
1957	2281	1.610967	TGACGGGCCATGTGAGGTA	60.611	57.895	4.39	0.00	0.00	3.08
1958	2282	1.144057	GACGGGCCATGTGAGGTAG	59.856	63.158	4.39	0.00	0.00	3.18
1959	2283	1.305802	ACGGGCCATGTGAGGTAGA	60.306	57.895	4.39	0.00	0.00	2.59
1960	2284	0.907704	ACGGGCCATGTGAGGTAGAA	60.908	55.000	4.39	0.00	0.00	2.10
1961	2285	0.462047	CGGGCCATGTGAGGTAGAAC	60.462	60.000	4.39	0.00	0.00	3.01
1962	2286	0.107165	GGGCCATGTGAGGTAGAACC	60.107	60.000	4.39	0.00	38.99	3.62
2058	2382	9.880157	ATCCAAGAATCTTCATAAAACAAATGG	57.120	29.630	0.00	0.00	0.00	3.16
2097	5145	9.467258	CCATGCCACTTTATTAAATAACTGATG	57.533	33.333	0.00	0.00	0.00	3.07
2182	5969	5.618056	TGCTTAAGCTTCAGTGATTCTTG	57.382	39.130	26.90	3.94	42.66	3.02
2304	6091	1.268265	TCTTGTGAATCGTCGCATCG	58.732	50.000	0.00	0.00	43.64	3.84

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
8	9	9.872684	ATCTTCCCAAATATTGATGTTATGTCT	57.127	29.630	0.00	0.00	0.00	3.41
177	180	3.756434	TGGGATTGAAAGAATCCGTTGTC	59.244	43.478	7.23	0.00	45.55	3.18
384	387	8.826710	GCCATAAAAATATTTTGACTTTAGCCC	58.173	33.333	14.04	0.00	0.00	5.19
582	587	3.931468	CACGATCAATCTCACAAGCTCTT	59.069	43.478	0.00	0.00	0.00	2.85
682	687	6.599445	ACCAAGCAGAGATAGCTATCATTTT	58.401	36.000	30.52	13.76	42.53	1.82
759	764	3.694364	CCCATTGAGATCTGGGTCG	57.306	57.895	0.00	0.00	46.01	4.79
918	925	2.435805	GTCTCTCAATACTGCCCCATCA	59.564	50.000	0.00	0.00	0.00	3.07
958	967	5.254032	AGTCTATTTTTCCATTCCCTCCTGT	59.746	40.000	0.00	0.00	0.00	4.00
975	984	3.795623	ACGTCCGCACAATAGTCTATT	57.204	42.857	0.00	0.00	0.00	1.73
984	993	0.948623	CCATGAGAACGTCCGCACAA	60.949	55.000	0.00	0.00	0.00	3.33
1079	1088	3.010420	GTCTTAACCACCTCCAGATTGC	58.990	50.000	0.00	0.00	0.00	3.56
1096	1105	1.347707	TCCTCCGTCTTGCATTGTCTT	59.652	47.619	0.00	0.00	0.00	3.01
1284	1293	7.015226	TGTGAGAAGTGTTACAATTTCACTG	57.985	36.000	24.89	0.00	41.37	3.66
1363	1372	2.014068	GCTAGCTCCAGGCATCGTTTT	61.014	52.381	7.70	0.00	44.79	2.43
1364	1373	0.462759	GCTAGCTCCAGGCATCGTTT	60.463	55.000	7.70	0.00	44.79	3.60
1365	1374	1.144936	GCTAGCTCCAGGCATCGTT	59.855	57.895	7.70	0.00	44.79	3.85
1390	1399	2.887152	GACATGAATAGGCCATCCAACC	59.113	50.000	5.01	0.00	33.74	3.77
1397	1406	3.435457	CCAATGAGGACATGAATAGGCCA	60.435	47.826	5.01	0.00	41.22	5.36
1483	1498	4.434989	CCAACAAATTGCATGCATCTTTCG	60.435	41.667	23.37	18.10	34.17	3.46
1484	1499	4.691685	TCCAACAAATTGCATGCATCTTTC	59.308	37.500	23.37	0.00	34.17	2.62
1485	1500	4.643463	TCCAACAAATTGCATGCATCTTT	58.357	34.783	23.37	20.14	34.17	2.52
1532	1553	7.561556	TCTGACTAACGAAAGAAACGATTTTC	58.438	34.615	0.00	0.00	41.44	2.29
1533	1554	7.473027	TCTGACTAACGAAAGAAACGATTTT	57.527	32.000	0.00	0.00	34.70	1.82
1534	1555	7.653767	ATCTGACTAACGAAAGAAACGATTT	57.346	32.000	0.00	0.00	34.70	2.17
1537	1558	6.580041	GTGTATCTGACTAACGAAAGAAACGA	59.420	38.462	0.00	0.00	34.70	3.85
1538	1559	6.450796	CGTGTATCTGACTAACGAAAGAAACG	60.451	42.308	0.00	0.00	0.00	3.60
1551	1745	5.417894	TCCACAGTAATTCGTGTATCTGACT	59.582	40.000	0.00	0.00	0.00	3.41
1572	1766	1.535444	TCTGCCCTTCTCCGTTCCA	60.535	57.895	0.00	0.00	0.00	3.53
1578	1772	1.066502	GTGAAGTCTCTGCCCTTCTCC	60.067	57.143	0.00	0.00	38.30	3.71
1585	1779	2.224161	ACAGAAGTGTGAAGTCTCTGCC	60.224	50.000	0.00	0.00	34.75	4.85
1618	1901	7.754625	TCAATCTTTTACGGTGCTATAAAACC	58.245	34.615	0.00	0.00	0.00	3.27
1640	1923	7.458397	ACTTATGTGTTCTACTCCCATTTCAA	58.542	34.615	0.00	0.00	0.00	2.69
1769	2056	3.006967	TCTTCAGCTGTGGAGACTTTACC	59.993	47.826	14.67	0.00	32.82	2.85
1772	2059	4.070716	CAATCTTCAGCTGTGGAGACTTT	58.929	43.478	14.67	5.74	41.46	2.66
1819	2106	3.818210	TGACAGAAAATTGAGCGCCTTTA	59.182	39.130	2.29	0.00	0.00	1.85
1887	2186	7.569240	TGTACTCAAACAAATTCCCCAAAAAT	58.431	30.769	0.00	0.00	0.00	1.82
1948	2271	6.550108	ACATATTCTACGGTTCTACCTCACAT	59.450	38.462	0.00	0.00	35.66	3.21
1955	2279	9.557338	CTGCTAATACATATTCTACGGTTCTAC	57.443	37.037	0.00	0.00	0.00	2.59
1956	2280	9.511272	TCTGCTAATACATATTCTACGGTTCTA	57.489	33.333	0.00	0.00	0.00	2.10
1957	2281	8.405418	TCTGCTAATACATATTCTACGGTTCT	57.595	34.615	0.00	0.00	0.00	3.01
1958	2282	9.640963	ATTCTGCTAATACATATTCTACGGTTC	57.359	33.333	0.00	0.00	0.00	3.62
1959	2283	9.640963	GATTCTGCTAATACATATTCTACGGTT	57.359	33.333	0.00	0.00	0.00	4.44
1960	2284	8.803235	TGATTCTGCTAATACATATTCTACGGT	58.197	33.333	0.00	0.00	0.00	4.83
1961	2285	9.639601	TTGATTCTGCTAATACATATTCTACGG	57.360	33.333	0.00	0.00	0.00	4.02
2058	2382	4.189231	AGTGGCATGGTCGTATTTAACTC	58.811	43.478	0.00	0.00	0.00	3.01
2068	2395	7.643764	CAGTTATTTAATAAAGTGGCATGGTCG	59.356	37.037	0.00	0.00	0.00	4.79
2097	5145	6.969828	ATAGAAAAGTGAGAAATGACGACC	57.030	37.500	0.00	0.00	0.00	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.