AutoCloner

Multiple sequence alignment - TraesCS1B01G013800

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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	TraesCS1B01G013800	chr1B	100.000	2258	0	0	1	2258	6461786	6464043	0.000000e+00	4170.0
1	TraesCS1B01G013800	chr1D	89.212	1205	65	21	661	1807	3801607	3802804	0.000000e+00	1445.0
2	TraesCS1B01G013800	chr1D	91.988	674	40	5	1	661	3800889	3801561	0.000000e+00	933.0
3	TraesCS1B01G013800	chr1D	89.249	679	51	6	1	661	3874178	3874852	0.000000e+00	830.0
4	TraesCS1B01G013800	chr1D	89.297	626	43	2	878	1485	3875084	3875703	0.000000e+00	763.0
5	TraesCS1B01G013800	chr1D	92.517	441	29	2	1820	2258	3803549	3803987	1.470000e-176	628.0
6	TraesCS1B01G013800	chr1D	91.176	68	6	0	1866	1933	3875941	3876008	2.390000e-15	93.5
7	TraesCS1B01G013800	chr1A	89.112	1194	62	25	661	1807	5332384	5333556	0.000000e+00	1423.0
8	TraesCS1B01G013800	chr1A	89.019	1193	64	25	661	1807	5367750	5368921	0.000000e+00	1415.0
9	TraesCS1B01G013800	chr1A	88.945	1194	65	28	661	1807	5246416	5247589	0.000000e+00	1411.0
10	TraesCS1B01G013800	chr1A	88.349	1193	63	23	661	1807	5176955	5178117	0.000000e+00	1363.0
11	TraesCS1B01G013800	chr1A	88.003	1192	66	30	661	1806	5195055	5196215	0.000000e+00	1338.0
12	TraesCS1B01G013800	chr1A	88.235	680	57	7	1	661	5194334	5195009	0.000000e+00	791.0
13	TraesCS1B01G013800	chr1A	87.941	680	59	7	1	661	5176234	5176909	0.000000e+00	780.0
14	TraesCS1B01G013800	chr1A	92.584	418	28	3	1820	2237	5197179	5197593	4.150000e-167	597.0
15	TraesCS1B01G013800	chr1A	92.344	418	29	3	1820	2237	5248546	5248960	1.930000e-165	592.0
16	TraesCS1B01G013800	chr1A	85.877	439	36	7	241	661	5245940	5246370	5.720000e-121	444.0
17	TraesCS1B01G013800	chr1A	85.194	439	39	7	241	661	5331908	5332338	5.760000e-116	427.0
18	TraesCS1B01G013800	chr1A	85.194	439	39	7	241	661	5367274	5367704	5.760000e-116	427.0
19	TraesCS1B01G013800	chrUn	89.112	1194	61	26	661	1807	85956	84785	0.000000e+00	1421.0
20	TraesCS1B01G013800	chrUn	89.038	1195	61	27	661	1807	281343737	281342565	0.000000e+00	1417.0
21	TraesCS1B01G013800	chrUn	90.046	864	46	17	661	1504	231646234	231645391	0.000000e+00	1083.0
22	TraesCS1B01G013800	chrUn	85.355	437	38	7	241	659	231646710	231646282	1.600000e-116	429.0
23	TraesCS1B01G013800	chrUn	85.194	439	39	7	241	661	86432	86002	5.760000e-116	427.0
24	TraesCS1B01G013800	chrUn	85.194	439	39	7	241	661	281344213	281343783	5.760000e-116	427.0
25	TraesCS1B01G013800	chrUn	86.230	305	14	12	1529	1807	373991906	373991604	2.820000e-79	305.0
26	TraesCS1B01G013800	chr3A	82.656	369	30	19	1484	1822	475723314	475722950	1.700000e-76	296.0
27	TraesCS1B01G013800	chr2B	79.167	312	53	11	1492	1796	661838203	661837897	2.940000e-49	206.0
28	TraesCS1B01G013800	chr2B	78.248	331	36	14	1486	1790	259008805	259009125	1.780000e-41	180.0
29	TraesCS1B01G013800	chr7D	76.344	372	32	26	1487	1807	237402872	237402506	5.020000e-32	148.0
30	TraesCS1B01G013800	chr7B	85.000	100	15	0	1672	1771	592339808	592339907	3.970000e-18	102.0

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	TraesCS1B01G013800	chr1B	6461786	6464043	2257	False	4170.000000	4170	100.000000	1	2258	1	chr1B.!!$F1	2257
1	TraesCS1B01G013800	chr1D	3800889	3803987	3098	False	1002.000000	1445	91.239000	1	2258	3	chr1D.!!$F1	2257
2	TraesCS1B01G013800	chr1D	3874178	3876008	1830	False	562.166667	830	89.907333	1	1933	3	chr1D.!!$F2	1932
3	TraesCS1B01G013800	chr1A	5176234	5178117	1883	False	1071.500000	1363	88.145000	1	1807	2	chr1A.!!$F1	1806
4	TraesCS1B01G013800	chr1A	5331908	5333556	1648	False	925.000000	1423	87.153000	241	1807	2	chr1A.!!$F4	1566
5	TraesCS1B01G013800	chr1A	5367274	5368921	1647	False	921.000000	1415	87.106500	241	1807	2	chr1A.!!$F5	1566
6	TraesCS1B01G013800	chr1A	5194334	5197593	3259	False	908.666667	1338	89.607333	1	2237	3	chr1A.!!$F2	2236
7	TraesCS1B01G013800	chr1A	5245940	5248960	3020	False	815.666667	1411	89.055333	241	2237	3	chr1A.!!$F3	1996
8	TraesCS1B01G013800	chrUn	84785	86432	1647	True	924.000000	1421	87.153000	241	1807	2	chrUn.!!$R2	1566
9	TraesCS1B01G013800	chrUn	281342565	281344213	1648	True	922.000000	1417	87.116000	241	1807	2	chrUn.!!$R4	1566
10	TraesCS1B01G013800	chrUn	231645391	231646710	1319	True	756.000000	1083	87.700500	241	1504	2	chrUn.!!$R3	1263

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
111	112	0.994247	AAGCAGTGGTGATGATGGGA	59.006	50.0	0.0	0.0	0.0	4.37	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1466	1570	0.035725	CCAGCATGAGCAGGTCAGAA	60.036	55.0	8.56	0.0	42.08	3.02	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
32	33	7.247456	TGTAAGAGTGGATGTTGGTATTGTA	57.753	36.000	0.00	0.00	0.00	2.41
78	79	8.372459	AGTTTGAAAAATTAATTGGGAGGGTAC	58.628	33.333	0.39	0.00	0.00	3.34
111	112	0.994247	AAGCAGTGGTGATGATGGGA	59.006	50.000	0.00	0.00	0.00	4.37
252	253	8.059798	AGGTGAATTATATAATGCTTGCATCC	57.940	34.615	13.59	7.31	0.00	3.51
335	340	2.924880	GCAACATACGGAAAAAGGCACC	60.925	50.000	0.00	0.00	0.00	5.01
357	362	1.203523	ACAGGTGCACGAGAGATCTTC	59.796	52.381	11.45	0.00	0.00	2.87
401	406	3.000727	GGTACAACACGAGCTTTGCTAT	58.999	45.455	0.00	0.00	39.88	2.97
406	411	2.893637	ACACGAGCTTTGCTATACCTG	58.106	47.619	0.00	0.00	39.88	4.00
413	418	2.618368	TTTGCTATACCTGCGGGGGC	62.618	60.000	18.00	14.45	40.03	5.80
415	420	3.060866	CTATACCTGCGGGGGCTC	58.939	66.667	18.00	0.00	40.03	4.70
416	421	2.915659	TATACCTGCGGGGGCTCG	60.916	66.667	18.00	0.00	40.03	5.03
417	422	3.744003	TATACCTGCGGGGGCTCGT	62.744	63.158	18.00	0.00	40.03	4.18
440	447	1.206878	GGGAGGGGGTTACGTAATGT	58.793	55.000	11.86	0.00	0.00	2.71
445	452	2.821378	AGGGGGTTACGTAATGTTTTGC	59.179	45.455	11.86	0.00	0.00	3.68
465	472	9.384682	GTTTTGCCAATTTCTAATTGTTCATTG	57.615	29.630	10.29	0.00	0.00	2.82
679	746	5.904941	ACAATTCTCATGTCAAAGTGCAAA	58.095	33.333	0.00	0.00	0.00	3.68
860	940	3.504520	GCTAGCTAGCTAGTTCTGGGTAG	59.495	52.174	39.05	21.90	45.67	3.18
1079	1161	3.455469	GAACATGGGCCAGCCTGC	61.455	66.667	13.78	0.00	36.10	4.85
1237	1319	3.508840	GTGGCACATGCTACGGCC	61.509	66.667	13.86	0.00	44.52	6.13
1466	1570	6.432162	TGCTTTCTGCTTCTTTCTATCATGTT	59.568	34.615	0.00	0.00	43.37	2.71
1473	1577	6.372659	TGCTTCTTTCTATCATGTTTCTGACC	59.627	38.462	0.00	0.00	0.00	4.02
1601	1717	3.000041	TGGATGTTCACAAGACATACGC	59.000	45.455	0.00	0.00	0.00	4.42
1749	1891	7.638444	TCAATAGGTATCTCAAATTTGGGTCA	58.362	34.615	17.50	4.28	0.00	4.02
1752	1894	5.501156	AGGTATCTCAAATTTGGGTCAGAC	58.499	41.667	17.50	6.93	0.00	3.51
1754	1896	5.586643	GGTATCTCAAATTTGGGTCAGACTC	59.413	44.000	17.50	9.21	0.00	3.36
1770	1912	3.762823	CAGACTCTTTTAGGGGTCGTAGT	59.237	47.826	0.00	0.00	34.34	2.73
1790	1932	6.975197	CGTAGTCATATGTCTTGTGAACATCT	59.025	38.462	7.79	0.00	0.00	2.90
1889	2995	0.179020	TCCGCCATCATGGATTGGAC	60.179	55.000	8.30	0.00	40.96	4.02
1922	3028	0.329261	TGGGGCTGGTTCATCTGAAG	59.671	55.000	0.00	0.00	34.27	3.02
1928	3034	2.354259	CTGGTTCATCTGAAGTGCTCC	58.646	52.381	0.00	0.00	34.27	4.70
1979	3085	7.288852	TCCTAAGAAATTGGACCAATGTTTTCA	59.711	33.333	23.98	10.84	34.04	2.69
1986	3092	5.957842	TGGACCAATGTTTTCATACTGAC	57.042	39.130	0.00	0.00	39.94	3.51
2003	3109	9.745880	TCATACTGACGAATTTAGGAATAGTTC	57.254	33.333	0.00	0.00	0.00	3.01
2030	3136	9.681692	TGCTGCATTTTGTTCATTGATATATAC	57.318	29.630	0.00	0.00	0.00	1.47
2088	3194	3.244735	TGCCAGCAAGTTAGTAACCATCA	60.245	43.478	9.46	0.00	0.00	3.07
2106	3212	4.318903	CCATCACTTACACGCGTTAACAAA	60.319	41.667	10.22	0.00	0.00	2.83
2114	3220	4.523813	ACACGCGTTAACAAATTCTTCTG	58.476	39.130	10.22	0.00	0.00	3.02
2172	3280	6.492429	TGTCAAGTGGTAGTAGCTTCTTCTAA	59.508	38.462	0.00	0.00	0.00	2.10
2202	3310	5.416639	TCAACTCCATTCACCAATCATTCAG	59.583	40.000	0.00	0.00	0.00	3.02
2218	3326	7.891498	ATCATTCAGGATCATGACAAATCAA	57.109	32.000	10.08	0.00	38.69	2.57

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
78	79	2.985809	CACTGCTTCAACTCTCTCTTCG	59.014	50.000	0.00	0.00	0.00	3.79
111	112	3.958147	CTCTGTCGGCGCCATGGTT	62.958	63.158	28.98	0.00	0.00	3.67
160	161	1.153756	CCAGTGCCACCTCCCTTTT	59.846	57.895	0.00	0.00	0.00	2.27
174	175	1.149101	ACACCCAGACCAATTCCAGT	58.851	50.000	0.00	0.00	0.00	4.00
229	230	7.972277	CCTGGATGCAAGCATTATATAATTCAC	59.028	37.037	9.16	0.00	36.70	3.18
252	253	4.986034	TGTACATCGACACTTGTAAACCTG	59.014	41.667	0.00	0.00	30.59	4.00
286	287	9.080097	GTTAGTTAGGGCTCTCTCTATTCATTA	57.920	37.037	0.00	0.00	0.00	1.90
335	340	0.459237	GATCTCTCGTGCACCTGTGG	60.459	60.000	12.15	0.00	0.00	4.17
357	362	5.416326	CCATAGTCCTTAGAGGTTAGGATCG	59.584	48.000	0.00	0.00	42.27	3.69
415	420	2.608368	TAACCCCCTCCCCACACG	60.608	66.667	0.00	0.00	0.00	4.49
416	421	2.963101	CGTAACCCCCTCCCCACAC	61.963	68.421	0.00	0.00	0.00	3.82
417	422	2.104359	TACGTAACCCCCTCCCCACA	62.104	60.000	0.00	0.00	0.00	4.17
440	447	8.566260	CCAATGAACAATTAGAAATTGGCAAAA	58.434	29.630	3.01	0.00	38.09	2.44
445	452	6.594937	CCCACCAATGAACAATTAGAAATTGG	59.405	38.462	14.87	15.42	46.14	3.16
536	548	5.968387	AACATGCTAGAACTACGTAATGC	57.032	39.130	0.00	0.00	0.00	3.56
631	652	3.006859	GTCTTTGCCATTTGCTAACCCTT	59.993	43.478	0.00	0.00	42.00	3.95
679	746	4.603989	TTGTGCACCAATGATTGAATGT	57.396	36.364	15.69	0.00	0.00	2.71
813	893	3.369892	GCTAGCATTCTTTCTCCACCTCA	60.370	47.826	10.63	0.00	0.00	3.86
841	921	3.558033	GACTACCCAGAACTAGCTAGCT	58.442	50.000	23.12	23.12	0.00	3.32
842	922	2.624364	GGACTACCCAGAACTAGCTAGC	59.376	54.545	20.91	6.62	34.14	3.42
843	923	4.139038	GAGGACTACCCAGAACTAGCTAG	58.861	52.174	19.44	19.44	37.41	3.42
844	924	3.526430	TGAGGACTACCCAGAACTAGCTA	59.474	47.826	0.00	0.00	37.41	3.32
845	925	2.312140	TGAGGACTACCCAGAACTAGCT	59.688	50.000	0.00	0.00	37.41	3.32
852	932	1.254026	CAACGTGAGGACTACCCAGA	58.746	55.000	0.00	0.00	37.41	3.86
860	940	2.167398	TAGGCAGCCAACGTGAGGAC	62.167	60.000	15.80	3.19	0.00	3.85
933	1015	1.417288	TGCGATGGATGGAGATGAGT	58.583	50.000	0.00	0.00	0.00	3.41
1079	1161	2.144833	TTTGCATTCTGTGGCTGCCG	62.145	55.000	14.98	0.00	35.02	5.69
1237	1319	1.841302	TAGCAGAAGTGGGCACAGGG	61.841	60.000	0.00	0.00	0.00	4.45
1280	1362	1.067974	CGAGGTACCAACACACACAGA	59.932	52.381	15.94	0.00	0.00	3.41
1466	1570	0.035725	CCAGCATGAGCAGGTCAGAA	60.036	55.000	8.56	0.00	42.08	3.02
1473	1577	2.280404	ATCCACCCCAGCATGAGCAG	62.280	60.000	0.00	0.00	45.49	4.24
1601	1717	9.640952	TTGATCTGAATTTTTAGGGGTTATAGG	57.359	33.333	0.00	0.00	0.00	2.57
1735	1877	6.396829	AAAAGAGTCTGACCCAAATTTGAG	57.603	37.500	19.86	9.10	0.00	3.02
1749	1891	4.015764	GACTACGACCCCTAAAAGAGTCT	58.984	47.826	0.00	0.00	31.47	3.24
1752	1894	6.040616	ACATATGACTACGACCCCTAAAAGAG	59.959	42.308	10.38	0.00	0.00	2.85
1754	1896	6.040616	AGACATATGACTACGACCCCTAAAAG	59.959	42.308	10.38	0.00	0.00	2.27
1770	1912	9.154847	CTTTGTAGATGTTCACAAGACATATGA	57.845	33.333	10.38	0.00	36.13	2.15
1822	1975	9.217278	CATGGATGGATATTTATGCTAGCTATC	57.783	37.037	17.23	13.43	0.00	2.08
1838	2944	6.158344	GGAAGAAGGATCTATCATGGATGGAT	59.842	42.308	4.96	4.96	41.70	3.41
1839	2945	5.486775	GGAAGAAGGATCTATCATGGATGGA	59.513	44.000	0.00	0.00	33.77	3.41
1889	2995	1.372307	CCCCAAAGCCAAAGCCAAG	59.628	57.895	0.00	0.00	41.25	3.61
1928	3034	2.665165	AGGTCAGAGCTCTATGTCTGG	58.335	52.381	17.75	1.85	40.61	3.86
1979	3085	9.751542	CAGAACTATTCCTAAATTCGTCAGTAT	57.248	33.333	0.00	0.00	0.00	2.12
1986	3092	5.294306	TGCAGCAGAACTATTCCTAAATTCG	59.706	40.000	0.00	0.00	0.00	3.34
2003	3109	8.812147	ATATATCAATGAACAAAATGCAGCAG	57.188	30.769	0.00	0.00	0.00	4.24
2030	3136	3.306088	CCACTTATACACTGCCCTATCCG	60.306	52.174	0.00	0.00	0.00	4.18
2088	3194	5.662211	AGAATTTGTTAACGCGTGTAAGT	57.338	34.783	14.98	0.00	0.00	2.24
2172	3280	6.891361	TGATTGGTGAATGGAGTTGACATTAT	59.109	34.615	0.00	0.00	38.57	1.28
2202	3310	6.521151	ACCTTCTTTGATTTGTCATGATCC	57.479	37.500	0.00	0.00	0.00	3.36

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.