AutoCloner

Multiple sequence alignment - TraesCS6B01G190400

Loading Multiple Alignment...

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	TraesCS6B01G190400	chr6B	100.000	2639	0	0	1	2639	223247731	223250369	0.000000e+00	4874.0
1	TraesCS6B01G190400	chr6B	91.032	2219	179	10	1	2203	567118188	567115974	0.000000e+00	2977.0
2	TraesCS6B01G190400	chr6B	91.828	2019	145	9	1	2002	147950688	147948673	0.000000e+00	2796.0
3	TraesCS6B01G190400	chr6B	81.421	549	71	15	1897	2419	567116157	567115614	1.130000e-113	420.0
4	TraesCS6B01G190400	chr3D	90.720	2457	187	18	1	2419	558679302	558681755	0.000000e+00	3236.0
5	TraesCS6B01G190400	chr4B	88.754	2463	225	28	1	2419	622503281	622500827	0.000000e+00	2966.0
6	TraesCS6B01G190400	chr5B	88.257	2444	247	31	1	2419	529280455	529282883	0.000000e+00	2887.0
7	TraesCS6B01G190400	chr5B	89.873	158	11	4	2267	2419	575025523	575025366	5.760000e-47	198.0
8	TraesCS6B01G190400	chr5B	78.571	182	33	6	1896	2074	529282468	529282646	5.970000e-22	115.0
9	TraesCS6B01G190400	chr5B	80.583	103	16	4	1981	2081	575035659	575035559	2.820000e-10	76.8
10	TraesCS6B01G190400	chr2B	88.226	2446	245	31	1	2419	664330485	664328056	0.000000e+00	2881.0
11	TraesCS6B01G190400	chr2B	77.249	189	37	5	1896	2081	664328474	664328289	3.590000e-19	106.0
12	TraesCS6B01G190400	chr5D	88.468	2428	215	41	1	2407	387241778	387244161	0.000000e+00	2872.0
13	TraesCS6B01G190400	chr5D	81.525	341	40	13	2312	2639	391236498	391236828	2.610000e-65	259.0
14	TraesCS6B01G190400	chr5D	78.297	364	58	14	2289	2636	387244100	387244458	5.720000e-52	215.0
15	TraesCS6B01G190400	chr3B	89.925	2253	184	20	1	2218	718831358	718829114	0.000000e+00	2863.0
16	TraesCS6B01G190400	chr3B	88.252	698	56	13	1957	2639	718829257	718828571	0.000000e+00	811.0
17	TraesCS6B01G190400	chr3B	84.528	265	36	5	2378	2639	479885686	479885424	9.370000e-65	257.0
18	TraesCS6B01G190400	chr3B	86.842	190	22	2	2017	2203	718829453	718829264	2.660000e-50	209.0
19	TraesCS6B01G190400	chr3B	90.000	50	3	1	1952	1999	718829186	718829235	2.190000e-06	63.9
20	TraesCS6B01G190400	chr7B	88.944	2198	206	14	1	2165	636041723	636039530	0.000000e+00	2678.0
21	TraesCS6B01G190400	chr7B	89.810	2051	165	32	1	2045	36428067	36426055	0.000000e+00	2590.0
22	TraesCS6B01G190400	chr7B	82.051	663	92	13	1781	2419	316357586	316356927	8.310000e-150	540.0
23	TraesCS6B01G190400	chr7B	80.051	391	54	16	2036	2419	36426100	36425727	4.330000e-68	268.0
24	TraesCS6B01G190400	chr7B	77.320	194	35	3	2019	2203	636039816	636039623	3.590000e-19	106.0
25	TraesCS6B01G190400	chr7B	77.193	171	33	6	1914	2081	36426100	36425933	7.780000e-16	95.3
26	TraesCS6B01G190400	chr1D	88.466	1916	172	22	505	2397	491071255	491069366	0.000000e+00	2268.0
27	TraesCS6B01G190400	chr1D	88.718	195	18	4	2447	2639	372883428	372883620	4.390000e-58	235.0
28	TraesCS6B01G190400	chr1D	82.703	185	32	0	2019	2203	491069860	491069676	5.840000e-37	165.0
29	TraesCS6B01G190400	chr4D	86.082	194	25	2	2447	2639	343948132	343948324	9.570000e-50	207.0
30	TraesCS6B01G190400	chr7D	82.727	110	19	0	1972	2081	536967106	536967215	6.010000e-17	99.0

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	TraesCS6B01G190400	chr6B	223247731	223250369	2638	False	4874.000000	4874	100.000000	1	2639	1	chr6B.!!$F1	2638
1	TraesCS6B01G190400	chr6B	147948673	147950688	2015	True	2796.000000	2796	91.828000	1	2002	1	chr6B.!!$R1	2001
2	TraesCS6B01G190400	chr6B	567115614	567118188	2574	True	1698.500000	2977	86.226500	1	2419	2	chr6B.!!$R2	2418
3	TraesCS6B01G190400	chr3D	558679302	558681755	2453	False	3236.000000	3236	90.720000	1	2419	1	chr3D.!!$F1	2418
4	TraesCS6B01G190400	chr4B	622500827	622503281	2454	True	2966.000000	2966	88.754000	1	2419	1	chr4B.!!$R1	2418
5	TraesCS6B01G190400	chr5B	529280455	529282883	2428	False	1501.000000	2887	83.414000	1	2419	2	chr5B.!!$F1	2418
6	TraesCS6B01G190400	chr2B	664328056	664330485	2429	True	1493.500000	2881	82.737500	1	2419	2	chr2B.!!$R1	2418
7	TraesCS6B01G190400	chr5D	387241778	387244458	2680	False	1543.500000	2872	83.382500	1	2636	2	chr5D.!!$F2	2635
8	TraesCS6B01G190400	chr3B	718828571	718831358	2787	True	1294.333333	2863	88.339667	1	2639	3	chr3B.!!$R2	2638
9	TraesCS6B01G190400	chr7B	636039530	636041723	2193	True	1392.000000	2678	83.132000	1	2203	2	chr7B.!!$R3	2202
10	TraesCS6B01G190400	chr7B	36425727	36428067	2340	True	984.433333	2590	82.351333	1	2419	3	chr7B.!!$R2	2418
11	TraesCS6B01G190400	chr7B	316356927	316357586	659	True	540.000000	540	82.051000	1781	2419	1	chr7B.!!$R1	638
12	TraesCS6B01G190400	chr1D	491069366	491071255	1889	True	1216.500000	2268	85.584500	505	2397	2	chr1D.!!$R1	1892

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
161	162	0.4546	GATCTACCAAGTGGACGCGA	59.545	55.0	15.93	0.0	38.94	5.87	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2074	2488	0.253044	GTGAGTTGCAGGGCCTATCA	59.747	55.0	5.28	4.36	0.0	2.15	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
34	35	2.128507	TTCCCAAACCACCGCCAAC	61.129	57.895	0.00	0.00	0.00	3.77
36	37	1.228306	CCCAAACCACCGCCAACTA	60.228	57.895	0.00	0.00	0.00	2.24
99	100	2.519013	GTTGAGGTTTCAAGCAGGGAT	58.481	47.619	0.00	0.00	43.66	3.85
159	160	2.604046	ATGATCTACCAAGTGGACGC	57.396	50.000	3.83	0.00	38.94	5.19
161	162	0.454600	GATCTACCAAGTGGACGCGA	59.545	55.000	15.93	0.00	38.94	5.87
193	194	2.104331	CGAGACGGCGTGGCTTAT	59.896	61.111	21.19	0.00	0.00	1.73
281	282	2.584143	GGCCATGCTCGCATTTGC	60.584	61.111	0.00	12.36	33.90	3.68
375	376	1.676968	CCACGAGGTTGACATGGGA	59.323	57.895	0.00	0.00	0.00	4.37
415	416	2.032681	GACCAGTCACAGTGGCCC	59.967	66.667	0.09	0.00	42.53	5.80
437	438	3.196469	CGAGTATGATGGCCCACATATCT	59.804	47.826	17.75	15.93	40.72	1.98
525	527	4.745351	TGGATGATCTAGCTGGATACACT	58.255	43.478	13.16	0.00	46.17	3.55
600	602	1.346068	TGTGGACAATGTGACGATCCA	59.654	47.619	0.00	0.00	37.11	3.41
618	620	3.248024	TCCAGGACACAATGTTAGGACT	58.752	45.455	0.00	0.00	0.00	3.85
770	772	3.388024	GCATGAGGTGGGACTACTATTCA	59.612	47.826	0.00	0.00	0.00	2.57
776	778	2.438021	GTGGGACTACTATTCATGGGCA	59.562	50.000	0.00	0.00	0.00	5.36
786	788	0.928505	TTCATGGGCATGGAGGACAT	59.071	50.000	0.00	0.00	41.57	3.06
804	806	2.652496	GCGAGTCTTAGAGGCGCG	60.652	66.667	11.70	0.00	45.71	6.86
806	808	2.470362	CGAGTCTTAGAGGCGCGGA	61.470	63.158	8.83	0.00	39.42	5.54
812	814	1.455032	TTAGAGGCGCGGATGGAGA	60.455	57.895	8.83	0.00	0.00	3.71
863	865	3.116395	AGGAGGATCAATAGAGGAAGGCT	60.116	47.826	0.00	0.00	36.25	4.58
898	901	4.709397	TGCTTAATCCGGATGGTTGAAATT	59.291	37.500	19.95	1.55	36.30	1.82
1085	1090	0.169009	GAGAATGCCAAACTGGACGC	59.831	55.000	0.00	0.00	40.96	5.19
1092	1097	1.234615	CCAAACTGGACGCGGTGAAT	61.235	55.000	12.47	0.00	40.96	2.57
1245	1250	2.423538	GCTTCCAACAAACGCCTATGAT	59.576	45.455	0.00	0.00	0.00	2.45
1434	1441	2.799017	TGTCTTAGGAGGCAACGACTA	58.201	47.619	0.00	0.00	46.39	2.59
1505	1512	4.755123	GGAGAAGATGGAACGAAAGAAACA	59.245	41.667	0.00	0.00	0.00	2.83
1537	1544	1.620323	GGGCATGCAAAGAGAAGGTTT	59.380	47.619	21.36	0.00	0.00	3.27
1557	1564	0.179150	CTCGTGAAGAAGAGAGGGCG	60.179	60.000	0.00	0.00	36.65	6.13
1657	1665	5.697178	CCTTAGTGATCTTGAGATGCATCTG	59.303	44.000	33.33	18.93	37.25	2.90
1678	1686	6.997655	TCTGTTGAAGTTGTATGTCTGAGAT	58.002	36.000	0.00	0.00	0.00	2.75
1809	1832	8.856490	ATTGTGAGACAAATTGTTACTGAAAC	57.144	30.769	0.00	0.00	41.96	2.78
1823	1846	8.251750	TGTTACTGAAACATTGTCAGCTATAC	57.748	34.615	5.63	0.00	45.35	1.47
1888	1916	3.495753	GCCTGTTTTTCATTTTGCAGAGG	59.504	43.478	0.00	0.00	0.00	3.69
1927	2079	1.603455	CCTGTGGCGGTTGGATGTT	60.603	57.895	0.00	0.00	0.00	2.71
1939	2091	1.078426	GGATGTTGCAGCCTACCGT	60.078	57.895	0.00	0.00	36.92	4.83
1949	2101	4.208686	CCTACCGTCGGAGGCAGC	62.209	72.222	20.51	0.00	33.69	5.25
1950	2102	3.449227	CTACCGTCGGAGGCAGCA	61.449	66.667	20.51	0.00	33.69	4.41
1977	2129	4.827087	CCTGCATCTCACGCGGCT	62.827	66.667	12.47	0.00	34.25	5.52
2003	2295	4.690153	ACCTTGTCTGGTGGGGAT	57.310	55.556	0.00	0.00	39.17	3.85
2007	2299	0.176680	CTTGTCTGGTGGGGATCGAG	59.823	60.000	0.00	0.00	0.00	4.04
2151	2592	1.003051	AAGGGATCCTACCGCCACT	59.997	57.895	12.58	0.00	31.13	4.00
2191	2632	2.642254	TTGCCTACCGTCGGAGGTG	61.642	63.158	20.51	4.40	45.54	4.00
2254	2717	5.921962	AAGGTTAGAGATGGCAAATTTCC	57.078	39.130	0.00	0.00	0.00	3.13
2364	2873	3.482436	TGAAATAAGAAGCAACACCCGT	58.518	40.909	0.00	0.00	0.00	5.28
2456	2965	4.755266	AGCATAAATTCTCTACACCGGT	57.245	40.909	0.00	0.00	0.00	5.28
2471	2980	3.754850	ACACCGGTAAAATGCTCCTAAAC	59.245	43.478	6.87	0.00	0.00	2.01
2505	3024	4.152402	GCTCAATTTGTTCTTCACGCTCTA	59.848	41.667	0.00	0.00	0.00	2.43
2564	3083	0.940126	GGCATAGCACATCCTTCACG	59.060	55.000	0.00	0.00	0.00	4.35
2607	3126	0.748450	ACGTCAGTTCGGGTTCTCAA	59.252	50.000	0.00	0.00	34.94	3.02

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
15	16	2.128507	TTGGCGGTGGTTTGGGAAC	61.129	57.895	0.00	0.00	34.96	3.62
99	100	2.777094	TGATTTGTTGATGCGAGGACA	58.223	42.857	0.00	0.00	0.00	4.02
127	128	9.739276	ACTTGGTAGATCATTTCTTTGTCATTA	57.261	29.630	0.00	0.00	35.79	1.90
159	160	2.881266	CGTGTTGTGCCACCTGTCG	61.881	63.158	0.00	0.00	31.47	4.35
161	162	1.523711	CTCGTGTTGTGCCACCTGT	60.524	57.895	0.00	0.00	31.47	4.00
193	194	1.002659	ACCTTATACGCAACACTGCCA	59.997	47.619	0.00	0.00	46.56	4.92
281	282	3.136123	CACCTTGGCCGCCATCAG	61.136	66.667	14.30	8.62	31.53	2.90
375	376	2.507471	AGGAAAGGATGAAATCGAGGCT	59.493	45.455	0.00	0.00	46.86	4.58
415	416	3.196469	AGATATGTGGGCCATCATACTCG	59.804	47.826	22.55	0.00	34.86	4.18
437	438	2.356432	CCATGAGTTCAGGATCAGGCAA	60.356	50.000	0.00	0.00	0.00	4.52
525	527	4.693566	CCGCTACCAAACTGTTTCATTCTA	59.306	41.667	2.13	0.00	0.00	2.10
600	602	3.181445	TGCAAGTCCTAACATTGTGTCCT	60.181	43.478	0.00	0.00	0.00	3.85
776	778	1.198713	AAGACTCGCATGTCCTCCAT	58.801	50.000	0.00	0.00	37.66	3.41
786	788	2.490217	GCGCCTCTAAGACTCGCA	59.510	61.111	0.00	0.00	44.50	5.10
804	806	2.502295	GAAGCATGACCATCTCCATCC	58.498	52.381	0.00	0.00	0.00	3.51
806	808	1.202734	CGGAAGCATGACCATCTCCAT	60.203	52.381	0.00	0.00	0.00	3.41
812	814	0.620556	AAGACCGGAAGCATGACCAT	59.379	50.000	9.46	0.00	0.00	3.55
863	865	5.411977	TCCGGATTAAGCAAAACGTCAATAA	59.588	36.000	0.00	0.00	0.00	1.40
1038	1043	2.444624	CGGCATGTCTTCACGGTCG	61.445	63.158	0.00	0.00	0.00	4.79
1085	1090	6.751888	GGTTTTCATATCCTTTTCATTCACCG	59.248	38.462	0.00	0.00	0.00	4.94
1092	1097	6.259893	TGATGGGGTTTTCATATCCTTTTCA	58.740	36.000	0.00	0.00	0.00	2.69
1245	1250	1.642112	TTGTCCATACCGGTGGTACA	58.358	50.000	19.93	13.28	41.31	2.90
1434	1441	5.105837	GCCTCTCTGAAATGCTTCTTCAAAT	60.106	40.000	0.00	0.00	32.57	2.32
1505	1512	2.364842	ATGCCCTCTCCTGCTCGT	60.365	61.111	0.00	0.00	0.00	4.18
1537	1544	1.178276	GCCCTCTCTTCTTCACGAGA	58.822	55.000	0.00	0.00	35.20	4.04
1557	1564	0.525311	GAGCCCTTGCAAGCTTTCTC	59.475	55.000	21.43	17.38	40.11	2.87
1657	1665	7.426929	ACAATCTCAGACATACAACTTCAAC	57.573	36.000	0.00	0.00	0.00	3.18
1678	1686	6.201997	CCGACATATGAAATACCATCGAACAA	59.798	38.462	10.38	0.00	34.50	2.83
1809	1832	7.922837	TCAACATTCATGTATAGCTGACAATG	58.077	34.615	7.30	8.97	40.80	2.82
1888	1916	2.873649	GCTATGGCAGTAGGGATGAAGC	60.874	54.545	0.00	0.00	38.54	3.86
1920	2072	1.078497	CGGTAGGCTGCAACATCCA	60.078	57.895	4.64	0.00	0.00	3.41
1927	2079	3.449227	CTCCGACGGTAGGCTGCA	61.449	66.667	14.79	0.00	0.00	4.41
1950	2102	3.866582	GATGCAGGGCCTACCGCT	61.867	66.667	5.28	0.00	46.96	5.52
2074	2488	0.253044	GTGAGTTGCAGGGCCTATCA	59.747	55.000	5.28	4.36	0.00	2.15
2076	2490	1.221840	CGTGAGTTGCAGGGCCTAT	59.778	57.895	5.28	0.00	0.00	2.57
2151	2592	2.041301	ACCCTACCGCCATAGCCA	60.041	61.111	0.00	0.00	34.57	4.75
2183	2624	2.601067	TAACGCCACCACCTCCGA	60.601	61.111	0.00	0.00	0.00	4.55
2185	2626	2.267961	CCTAACGCCACCACCTCC	59.732	66.667	0.00	0.00	0.00	4.30
2190	2631	1.493854	ATCAACCCCTAACGCCACCA	61.494	55.000	0.00	0.00	0.00	4.17
2191	2632	0.746923	GATCAACCCCTAACGCCACC	60.747	60.000	0.00	0.00	0.00	4.61
2295	2787	3.181463	TGAACTAAGTACCGGTGTTGCTT	60.181	43.478	19.93	17.32	0.00	3.91
2296	2788	2.366266	TGAACTAAGTACCGGTGTTGCT	59.634	45.455	19.93	7.18	0.00	3.91
2297	2789	2.758009	TGAACTAAGTACCGGTGTTGC	58.242	47.619	19.93	4.69	0.00	4.17
2298	2790	5.467399	TCATTTGAACTAAGTACCGGTGTTG	59.533	40.000	19.93	6.01	0.00	3.33
2300	2792	4.992951	GTCATTTGAACTAAGTACCGGTGT	59.007	41.667	19.93	2.25	0.00	4.16
2301	2793	4.992319	TGTCATTTGAACTAAGTACCGGTG	59.008	41.667	19.93	1.45	0.00	4.94
2456	2965	9.834628	CGTATCAAAAAGTTTAGGAGCATTTTA	57.165	29.630	0.00	0.00	0.00	1.52
2505	3024	5.759059	TGATATTCAACTCAGGCCAAATCT	58.241	37.500	5.01	0.00	0.00	2.40
2548	3067	0.530650	CGGCGTGAAGGATGTGCTAT	60.531	55.000	0.00	0.00	0.00	2.97

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.