AutoCloner

Multiple sequence alignment - TraesCS6B01G033200

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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	TraesCS6B01G033200	chr6B	100.000	2348	0	0	1	2348	19541774	19544121	0.000000e+00	4337
1	TraesCS6B01G033200	chr6B	93.706	143	9	0	2206	2348	484539644	484539502	5.080000e-52	215
2	TraesCS6B01G033200	chr7B	90.553	1789	131	13	65	1825	554784113	554785891	0.000000e+00	2333
3	TraesCS6B01G033200	chr7B	84.286	1871	234	40	3	1825	522605802	522603944	0.000000e+00	1772
4	TraesCS6B01G033200	chr7B	94.415	376	21	0	1831	2206	287934865	287935240	1.560000e-161	579
5	TraesCS6B01G033200	chr7B	94.430	377	20	1	1833	2208	307431489	307431113	1.560000e-161	579
6	TraesCS6B01G033200	chr7B	82.027	523	63	14	3	499	414092190	414092707	1.300000e-112	416
7	TraesCS6B01G033200	chr7B	93.706	143	6	2	2209	2348	654020411	654020269	6.570000e-51	211
8	TraesCS6B01G033200	chr7B	93.007	143	10	0	2206	2348	554785892	554786034	2.360000e-50	209
9	TraesCS6B01G033200	chr2B	89.584	1853	148	21	5	1825	424515238	424513399	0.000000e+00	2311
10	TraesCS6B01G033200	chr2B	86.495	1866	212	20	1	1829	243358806	243360668	0.000000e+00	2013
11	TraesCS6B01G033200	chr2B	84.533	1862	236	32	3	1825	547943785	547945633	0.000000e+00	1796
12	TraesCS6B01G033200	chr2B	94.444	378	21	0	1831	2208	625160552	625160175	1.210000e-162	582
13	TraesCS6B01G033200	chr2B	94.180	378	22	0	1831	2208	625162601	625162224	5.630000e-161	577
14	TraesCS6B01G033200	chr2B	93.007	143	10	0	2206	2348	355884460	355884602	2.360000e-50	209
15	TraesCS6B01G033200	chr4A	89.249	1851	158	10	3	1822	666800204	666802044	0.000000e+00	2278
16	TraesCS6B01G033200	chr4A	89.840	1496	141	9	335	1824	653709963	653708473	0.000000e+00	1910
17	TraesCS6B01G033200	chr4A	85.223	1658	217	16	189	1825	24864754	24863104	0.000000e+00	1679
18	TraesCS6B01G033200	chr7D	86.371	1849	216	27	3	1825	604446051	604444213	0.000000e+00	1986
19	TraesCS6B01G033200	chr7D	83.308	647	76	15	3	622	576160450	576159809	3.390000e-158	568
20	TraesCS6B01G033200	chr7D	86.893	206	24	3	3	207	638444698	638444901	6.530000e-56	228
21	TraesCS6B01G033200	chr5D	85.354	1864	217	31	3	1825	430529845	430531693	0.000000e+00	1879
22	TraesCS6B01G033200	chr3D	89.375	1440	138	9	397	1825	429293701	429295136	0.000000e+00	1797
23	TraesCS6B01G033200	chr3D	95.238	378	15	2	1830	2205	573446423	573446799	1.550000e-166	595
24	TraesCS6B01G033200	chr4D	84.124	1877	234	31	3	1829	293372235	293374097	0.000000e+00	1757
25	TraesCS6B01G033200	chr2D	83.778	1874	238	35	3	1825	586776435	586774577	0.000000e+00	1716
26	TraesCS6B01G033200	chr2D	93.750	384	21	3	1823	2205	295791842	295792223	7.280000e-160	573
27	TraesCS6B01G033200	chr5B	94.974	378	19	0	1831	2208	522854145	522853768	5.590000e-166	593
28	TraesCS6B01G033200	chr5B	94.667	375	20	0	1831	2205	522851201	522850827	1.210000e-162	582
29	TraesCS6B01G033200	chr5B	93.007	143	10	0	2206	2348	595076737	595076879	2.360000e-50	209
30	TraesCS6B01G033200	chr5B	93.571	140	9	0	2209	2348	653396644	653396505	2.360000e-50	209
31	TraesCS6B01G033200	chr6A	94.400	375	21	0	1831	2205	613599989	613600363	5.630000e-161	577
32	TraesCS6B01G033200	chr3B	97.143	140	4	0	2209	2348	8004083	8003944	1.080000e-58	237
33	TraesCS6B01G033200	chr4B	87.940	199	21	3	3	200	670894110	670893914	5.050000e-57	231
34	TraesCS6B01G033200	chr4B	93.706	143	9	0	2206	2348	516867678	516867820	5.080000e-52	215
35	TraesCS6B01G033200	chr1B	94.891	137	7	0	2212	2348	562439600	562439736	5.080000e-52	215

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	TraesCS6B01G033200	chr6B	19541774	19544121	2347	False	4337.0	4337	100.0000	1	2348	1	chr6B.!!$F1	2347
1	TraesCS6B01G033200	chr7B	522603944	522605802	1858	True	1772.0	1772	84.2860	3	1825	1	chr7B.!!$R2	1822
2	TraesCS6B01G033200	chr7B	554784113	554786034	1921	False	1271.0	2333	91.7800	65	2348	2	chr7B.!!$F3	2283
3	TraesCS6B01G033200	chr7B	414092190	414092707	517	False	416.0	416	82.0270	3	499	1	chr7B.!!$F2	496
4	TraesCS6B01G033200	chr2B	424513399	424515238	1839	True	2311.0	2311	89.5840	5	1825	1	chr2B.!!$R1	1820
5	TraesCS6B01G033200	chr2B	243358806	243360668	1862	False	2013.0	2013	86.4950	1	1829	1	chr2B.!!$F1	1828
6	TraesCS6B01G033200	chr2B	547943785	547945633	1848	False	1796.0	1796	84.5330	3	1825	1	chr2B.!!$F3	1822
7	TraesCS6B01G033200	chr2B	625160175	625162601	2426	True	579.5	582	94.3120	1831	2208	2	chr2B.!!$R2	377
8	TraesCS6B01G033200	chr4A	666800204	666802044	1840	False	2278.0	2278	89.2490	3	1822	1	chr4A.!!$F1	1819
9	TraesCS6B01G033200	chr4A	653708473	653709963	1490	True	1910.0	1910	89.8400	335	1824	1	chr4A.!!$R2	1489
10	TraesCS6B01G033200	chr4A	24863104	24864754	1650	True	1679.0	1679	85.2230	189	1825	1	chr4A.!!$R1	1636
11	TraesCS6B01G033200	chr7D	604444213	604446051	1838	True	1986.0	1986	86.3710	3	1825	1	chr7D.!!$R2	1822
12	TraesCS6B01G033200	chr7D	576159809	576160450	641	True	568.0	568	83.3080	3	622	1	chr7D.!!$R1	619
13	TraesCS6B01G033200	chr5D	430529845	430531693	1848	False	1879.0	1879	85.3540	3	1825	1	chr5D.!!$F1	1822
14	TraesCS6B01G033200	chr3D	429293701	429295136	1435	False	1797.0	1797	89.3750	397	1825	1	chr3D.!!$F1	1428
15	TraesCS6B01G033200	chr4D	293372235	293374097	1862	False	1757.0	1757	84.1240	3	1829	1	chr4D.!!$F1	1826
16	TraesCS6B01G033200	chr2D	586774577	586776435	1858	True	1716.0	1716	83.7780	3	1825	1	chr2D.!!$R1	1822
17	TraesCS6B01G033200	chr5B	522850827	522854145	3318	True	587.5	593	94.8205	1831	2208	2	chr5B.!!$R2	377

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
897	941	0.036388	ATCTTCGACGGTGGTGCATT	60.036	50.0	0.0	0.0	0.0	3.56	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2245	5338	0.105778	GAGCCTCCTCCTTTGGATCG	59.894	60.0	0.0	0.0	35.3	3.69	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
63	65	1.295423	CGGACGACCCATTTCTGGT	59.705	57.895	0.00	0.00	41.37	4.00
88	90	1.524848	TTTAAGCCGGATTTGCGTCA	58.475	45.000	11.69	0.00	0.00	4.35
159	162	4.680237	CGGTCGGTGGCAGCAAGA	62.680	66.667	17.80	3.73	0.00	3.02
282	317	1.450312	GGCATGAAGACCGTCCCTG	60.450	63.158	0.00	0.00	0.00	4.45
546	587	2.830285	AACACGGCCTTGTCAACGC	61.830	57.895	16.23	0.00	0.00	4.84
632	676	4.263572	CTTGCACCCCGACACCCA	62.264	66.667	0.00	0.00	0.00	4.51
737	781	2.511600	CGCCCATCGACCTCAACC	60.512	66.667	0.00	0.00	41.67	3.77
745	789	2.813726	CGACCTCAACCCCACACCA	61.814	63.158	0.00	0.00	0.00	4.17
767	811	2.187946	CCAGTGGCTCGTCATCCC	59.812	66.667	0.00	0.00	0.00	3.85
808	852	2.494445	CAGATGCCAGCCGACGTA	59.506	61.111	0.00	0.00	0.00	3.57
813	857	1.035932	ATGCCAGCCGACGTACTACT	61.036	55.000	0.00	0.00	0.00	2.57
897	941	0.036388	ATCTTCGACGGTGGTGCATT	60.036	50.000	0.00	0.00	0.00	3.56
900	949	2.358125	CGACGGTGGTGCATTGGA	60.358	61.111	0.00	0.00	0.00	3.53
1098	1155	2.687935	TGAAGTGGAGCCTTTGTTTGAC	59.312	45.455	0.00	0.00	0.00	3.18
1166	1223	1.739466	CAAGCACACGAAGGCATACAT	59.261	47.619	0.00	0.00	0.00	2.29
1168	1225	1.066215	AGCACACGAAGGCATACATGA	60.066	47.619	0.00	0.00	0.00	3.07
1263	1322	3.989817	AGCATTCAACTTTTTGGATTCGC	59.010	39.130	0.00	0.00	26.96	4.70
1320	1379	4.074970	CTCCTTACCAAATTGTGAGCACT	58.925	43.478	1.99	0.00	0.00	4.40
1374	1433	5.068636	AGAGTGATTCAACAAGAGTGCAAT	58.931	37.500	0.00	0.00	0.00	3.56
1456	1528	3.649981	AGACATGATATGGTAGCAAGCCT	59.350	43.478	0.00	0.00	33.60	4.58
1458	1530	3.649981	ACATGATATGGTAGCAAGCCTCT	59.350	43.478	0.00	0.00	33.60	3.69
1470	1543	3.071602	AGCAAGCCTCTCTCTTTTGTGTA	59.928	43.478	0.00	0.00	0.00	2.90
1484	1557	6.446318	TCTTTTGTGTAATCAAGTTCATGCC	58.554	36.000	0.00	0.00	0.00	4.40
1509	1586	3.368539	CGTGTTCATTTGCATCCCATTTG	59.631	43.478	0.00	0.00	0.00	2.32
1510	1587	4.317488	GTGTTCATTTGCATCCCATTTGT	58.683	39.130	0.00	0.00	0.00	2.83
1555	1634	3.302365	TGTAGGCATTTCAAGCTTTGC	57.698	42.857	11.60	11.60	0.00	3.68
1567	1646	1.335145	AGCTTTGCAGGCATTCAAGT	58.665	45.000	14.52	0.00	0.00	3.16
1621	1700	5.074929	TCCCATTGCTATAGGGTCATCAAAT	59.925	40.000	1.04	0.00	43.31	2.32
1778	1859	1.421410	GCATCGAACGCCTTGATCGT	61.421	55.000	0.00	0.00	42.79	3.73
1825	1907	2.000048	AGGACTCAAGAGAGGAGGAGT	59.000	52.381	3.73	0.00	46.44	3.85
1829	1911	2.109128	ACTCAAGAGAGGAGGAGTGTCA	59.891	50.000	3.73	0.00	46.44	3.58
1885	1967	6.209391	GGTAGGTTACAGTTGGACTTGTAGTA	59.791	42.308	0.00	0.00	0.00	1.82
1961	2043	2.245028	AGGCCTCTCATATATAGCGGGA	59.755	50.000	0.00	0.00	0.00	5.14
2001	2083	4.141274	ACCTATGCCAACATAATAGCACCA	60.141	41.667	0.00	0.00	38.29	4.17
2008	2090	2.201732	ACATAATAGCACCAGAACGCG	58.798	47.619	3.53	3.53	0.00	6.01
2062	2144	2.671914	GCGACCGAGTGTGGTATTGTAA	60.672	50.000	0.00	0.00	44.01	2.41
2147	5240	3.182972	CGTTAACAAATCTCGGTGTCGTT	59.817	43.478	6.39	0.00	37.69	3.85
2174	5267	1.281867	TGATTGCTTGGTCCTCGGATT	59.718	47.619	0.00	0.00	0.00	3.01
2212	5305	3.060740	GGATTTATTCTAACACGTCGGCG	60.061	47.826	8.42	8.42	44.93	6.46
2234	5327	4.676924	CGTTTCAAAGAGGAGCAAATGAAC	59.323	41.667	0.00	0.00	0.00	3.18
2244	5337	2.161855	AGCAAATGAACGCCTTCATGA	58.838	42.857	11.07	0.00	44.93	3.07
2245	5338	2.095059	AGCAAATGAACGCCTTCATGAC	60.095	45.455	11.07	5.06	44.93	3.06
2264	5357	0.105778	CGATCCAAAGGAGGAGGCTC	59.894	60.000	5.78	5.78	41.90	4.70
2270	5363	1.118838	AAAGGAGGAGGCTCGAGATG	58.881	55.000	18.75	0.00	0.00	2.90
2294	5387	0.731417	CGGAGAAGCAAGCCAAGATG	59.269	55.000	0.00	0.00	0.00	2.90
2310	5403	0.391661	GATGCTTGAGTTGGAGGCGA	60.392	55.000	0.00	0.00	0.00	5.54

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
63	65	3.674682	CGCAAATCCGGCTTAAAATTGGA	60.675	43.478	0.00	0.00	0.00	3.53
282	317	3.449227	GGGGCTTGCCTTTACCGC	61.449	66.667	11.71	0.00	0.00	5.68
286	321	2.675075	GCACGGGGCTTGCCTTTA	60.675	61.111	11.71	0.00	40.25	1.85
409	444	4.699522	GCGACGGCTTCACCCCTT	62.700	66.667	0.00	0.00	35.83	3.95
499	534	5.354842	GGTTTAACCCTAGCATGTAGAGT	57.645	43.478	2.04	0.00	30.04	3.24
529	564	3.276846	GCGTTGACAAGGCCGTGT	61.277	61.111	25.07	25.07	36.34	4.49
627	671	1.732259	GATACACGTGAAAGCTGGGTG	59.268	52.381	25.01	0.00	34.87	4.61
632	676	0.037697	TGCGGATACACGTGAAAGCT	60.038	50.000	25.01	0.85	35.98	3.74
737	781	1.003355	CACTGGCTACTGGTGTGGG	60.003	63.158	0.00	0.00	0.00	4.61
808	852	3.307906	TTGCGGGCGTCCAGTAGT	61.308	61.111	6.96	0.00	0.00	2.73
897	941	1.760875	GTCGGGGTCATAGCCTCCA	60.761	63.158	0.00	0.00	35.71	3.86
900	949	1.828660	CTCGTCGGGGTCATAGCCT	60.829	63.158	0.00	0.00	35.71	4.58
973	1029	0.392863	TGATCACACATGAAGGCCGG	60.393	55.000	0.00	0.00	38.69	6.13
1166	1223	4.373116	GCTTGTCCTCGGCCGTCA	62.373	66.667	27.15	16.84	0.00	4.35
1168	1225	3.591254	GAAGCTTGTCCTCGGCCGT	62.591	63.158	27.15	0.00	0.00	5.68
1263	1322	1.019278	CATGAAACTCCCGGTGGACG	61.019	60.000	0.00	0.00	43.80	4.79
1374	1433	4.776349	TCTCAAGAGTGGCACAAAACTTA	58.224	39.130	21.41	2.75	44.16	2.24
1441	1504	3.855668	AGAGAGAGGCTTGCTACCATAT	58.144	45.455	0.00	0.00	0.00	1.78
1456	1528	8.777413	CATGAACTTGATTACACAAAAGAGAGA	58.223	33.333	0.00	0.00	0.00	3.10
1458	1530	7.362662	GCATGAACTTGATTACACAAAAGAGA	58.637	34.615	0.00	0.00	0.00	3.10
1470	1543	1.200716	CACGCAGGCATGAACTTGATT	59.799	47.619	0.62	0.00	0.00	2.57
1484	1557	1.621107	GGATGCAAATGAACACGCAG	58.379	50.000	0.00	0.00	37.88	5.18
1509	1586	2.451693	CATGCAAGCATGTTGGCAC	58.548	52.632	23.25	0.00	46.20	5.01
1510	1587	4.999212	CATGCAAGCATGTTGGCA	57.001	50.000	23.25	14.50	46.20	4.92
1555	1634	5.437289	TTGTGTTAGAACTTGAATGCCTG	57.563	39.130	0.00	0.00	0.00	4.85
1567	1646	3.221771	AGCACTTGCCATTGTGTTAGAA	58.778	40.909	0.00	0.00	43.38	2.10
1621	1700	3.198068	GCGCCTTGAACTTCTCATCATA	58.802	45.455	0.00	0.00	32.78	2.15
1778	1859	0.179048	CATCATGCCCTCCACGCTTA	60.179	55.000	0.00	0.00	0.00	3.09
1825	1907	4.577834	TCGACACAACTCTAACATGACA	57.422	40.909	0.00	0.00	0.00	3.58
1829	1911	8.467598	ACACTATATTCGACACAACTCTAACAT	58.532	33.333	0.00	0.00	0.00	2.71
1898	1980	5.516059	AGGACACGACTCCATATCCTATA	57.484	43.478	6.01	0.00	34.77	1.31
1930	2012	9.647918	CTATATATGAGAGGCCTAGGATACAAA	57.352	37.037	14.75	0.00	41.41	2.83
1961	2043	5.450137	GCATAGGTTACATCGTGTGTCTACT	60.450	44.000	0.00	1.13	42.29	2.57
2048	2130	3.069872	TGACACCGTTACAATACCACACT	59.930	43.478	0.00	0.00	0.00	3.55
2052	2134	3.601435	CCATGACACCGTTACAATACCA	58.399	45.455	0.00	0.00	0.00	3.25
2062	2144	1.990060	CTCCTCCCCATGACACCGT	60.990	63.158	0.00	0.00	0.00	4.83
2147	5240	1.608025	GGACCAAGCAATCACACGAGA	60.608	52.381	0.00	0.00	0.00	4.04
2212	5305	4.676924	CGTTCATTTGCTCCTCTTTGAAAC	59.323	41.667	0.00	0.00	0.00	2.78
2244	5337	0.618968	AGCCTCCTCCTTTGGATCGT	60.619	55.000	0.00	0.00	35.30	3.73
2245	5338	0.105778	GAGCCTCCTCCTTTGGATCG	59.894	60.000	0.00	0.00	35.30	3.69
2264	5357	0.943359	GCTTCTCCGCATCCATCTCG	60.943	60.000	0.00	0.00	0.00	4.04
2270	5363	2.476320	GGCTTGCTTCTCCGCATCC	61.476	63.158	0.00	0.00	40.04	3.51
2294	5387	0.320771	TCTTCGCCTCCAACTCAAGC	60.321	55.000	0.00	0.00	0.00	4.01
2310	5403	1.818642	AGCATCTTCGCTTGCTTCTT	58.181	45.000	0.00	0.00	46.71	2.52

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.