AutoCloner

Multiple sequence alignment - TraesCS3A01G385800

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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	TraesCS3A01G385800	chr3A	100.000	2309	0	0	1	2309	635312056	635314364	0.000000e+00	4265.0
1	TraesCS3A01G385800	chr7A	95.600	2318	91	7	1	2309	38737226	38739541	0.000000e+00	3705.0
2	TraesCS3A01G385800	chr7A	96.632	1841	47	10	1	1835	124062144	124060313	0.000000e+00	3042.0
3	TraesCS3A01G385800	chr7A	94.002	1884	75	19	1	1848	192624593	192626474	0.000000e+00	2819.0
4	TraesCS3A01G385800	chr7A	93.587	1653	63	14	624	2269	134596514	134598130	0.000000e+00	2425.0
5	TraesCS3A01G385800	chr7A	90.698	1720	110	24	624	2309	699322353	699320650	0.000000e+00	2244.0
6	TraesCS3A01G385800	chr7A	97.730	837	19	0	1	837	134595861	134596697	0.000000e+00	1441.0
7	TraesCS3A01G385800	chr7A	94.359	390	22	0	1920	2309	192627323	192627712	1.180000e-167	599.0
8	TraesCS3A01G385800	chr7A	82.531	561	41	22	1776	2309	643611003	643611533	7.570000e-120	440.0
9	TraesCS3A01G385800	chr7A	94.326	282	16	0	2028	2309	124060304	124060023	1.270000e-117	433.0
10	TraesCS3A01G385800	chr7A	85.919	419	28	12	1510	1897	719951067	719950649	3.550000e-113	418.0
11	TraesCS3A01G385800	chr7A	93.750	176	11	0	1969	2144	192626470	192626645	4.890000e-67	265.0
12	TraesCS3A01G385800	chr7A	92.391	184	14	0	2126	2309	643611211	643611394	1.760000e-66	263.0
13	TraesCS3A01G385800	chr4A	96.251	1894	47	2	1	1894	637837312	637835443	0.000000e+00	3083.0
14	TraesCS3A01G385800	chr4A	94.915	236	12	0	2074	2309	637835438	637835203	1.010000e-98	370.0
15	TraesCS3A01G385800	chr6A	90.700	2344	122	33	1	2309	516298136	516295854	0.000000e+00	3033.0
16	TraesCS3A01G385800	chr1A	96.022	1785	64	5	1	1779	480958127	480959910	0.000000e+00	2896.0
17	TraesCS3A01G385800	chr1A	84.000	200	29	3	1997	2195	559591607	559591804	3.030000e-44	189.0
18	TraesCS3A01G385800	chr2A	94.255	1793	83	15	1	1779	372742755	372744541	0.000000e+00	2723.0
19	TraesCS3A01G385800	chr2A	84.559	544	40	18	1776	2309	677897567	677897058	1.230000e-137	499.0
20	TraesCS3A01G385800	chr2A	91.848	184	15	0	2126	2309	677897359	677897176	8.190000e-65	257.0
21	TraesCS3A01G385800	chr2A	79.537	259	28	10	1938	2195	677897289	677897055	6.600000e-36	161.0
22	TraesCS3A01G385800	chr2A	82.171	129	8	1	2196	2309	677897421	677897293	1.890000e-16	97.1
23	TraesCS3A01G385800	chr2A	85.938	64	9	0	2246	2309	372745011	372745074	4.120000e-08	69.4
24	TraesCS3A01G385800	chr2A	88.235	51	5	1	2082	2131	677897419	677897369	2.480000e-05	60.2
25	TraesCS3A01G385800	chr5D	93.757	1794	87	16	1	1776	387840690	387838904	0.000000e+00	2669.0
26	TraesCS3A01G385800	chr5A	95.833	1656	59	4	660	2309	606688455	606690106	0.000000e+00	2667.0
27	TraesCS3A01G385800	chr5A	97.252	837	23	0	1	837	288269189	288268353	0.000000e+00	1419.0

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	TraesCS3A01G385800	chr3A	635312056	635314364	2308	False	4265.000000	4265	100.0000	1	2309	1	chr3A.!!$F1	2308
1	TraesCS3A01G385800	chr7A	38737226	38739541	2315	False	3705.000000	3705	95.6000	1	2309	1	chr7A.!!$F1	2308
2	TraesCS3A01G385800	chr7A	699320650	699322353	1703	True	2244.000000	2244	90.6980	624	2309	1	chr7A.!!$R1	1685
3	TraesCS3A01G385800	chr7A	134595861	134598130	2269	False	1933.000000	2425	95.6585	1	2269	2	chr7A.!!$F2	2268
4	TraesCS3A01G385800	chr7A	124060023	124062144	2121	True	1737.500000	3042	95.4790	1	2309	2	chr7A.!!$R3	2308
5	TraesCS3A01G385800	chr7A	192624593	192627712	3119	False	1227.666667	2819	94.0370	1	2309	3	chr7A.!!$F3	2308
6	TraesCS3A01G385800	chr7A	643611003	643611533	530	False	351.500000	440	87.4610	1776	2309	2	chr7A.!!$F4	533
7	TraesCS3A01G385800	chr4A	637835203	637837312	2109	True	1726.500000	3083	95.5830	1	2309	2	chr4A.!!$R1	2308
8	TraesCS3A01G385800	chr6A	516295854	516298136	2282	True	3033.000000	3033	90.7000	1	2309	1	chr6A.!!$R1	2308
9	TraesCS3A01G385800	chr1A	480958127	480959910	1783	False	2896.000000	2896	96.0220	1	1779	1	chr1A.!!$F1	1778
10	TraesCS3A01G385800	chr2A	372742755	372745074	2319	False	1396.200000	2723	90.0965	1	2309	2	chr2A.!!$F1	2308
11	TraesCS3A01G385800	chr2A	677897055	677897567	512	True	214.860000	499	85.2700	1776	2309	5	chr2A.!!$R1	533
12	TraesCS3A01G385800	chr5D	387838904	387840690	1786	True	2669.000000	2669	93.7570	1	1776	1	chr5D.!!$R1	1775
13	TraesCS3A01G385800	chr5A	606688455	606690106	1651	False	2667.000000	2667	95.8330	660	2309	1	chr5A.!!$F1	1649
14	TraesCS3A01G385800	chr5A	288268353	288269189	836	True	1419.000000	1419	97.2520	1	837	1	chr5A.!!$R1	836

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
729	892	0.034059	AGAGGTGTTGGTCGAGCAAG	59.966	55.0	28.94	0.0	0.0	4.01	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2023	3180	0.878523	CCTGCGTGACCAAAACGAGA	60.879	55.0	0.0	0.0	43.68	4.04	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
51	52	4.272504	ACGGCAACAAGTTATCATATTCGG	59.727	41.667	0.00	0.00	0.00	4.30
504	505	3.954904	GAGGCTCCTGACACTATCAACTA	59.045	47.826	2.15	0.00	36.69	2.24
559	560	4.396166	CGGACATGCAAGAATAGGAAAACT	59.604	41.667	0.00	0.00	0.00	2.66
723	886	0.603569	AGTGCTAGAGGTGTTGGTCG	59.396	55.000	0.00	0.00	0.00	4.79
724	887	0.601558	GTGCTAGAGGTGTTGGTCGA	59.398	55.000	0.00	0.00	0.00	4.20
725	888	0.888619	TGCTAGAGGTGTTGGTCGAG	59.111	55.000	0.00	0.00	0.00	4.04
726	889	0.458716	GCTAGAGGTGTTGGTCGAGC	60.459	60.000	7.89	7.89	34.83	5.03
727	890	0.888619	CTAGAGGTGTTGGTCGAGCA	59.111	55.000	14.39	14.39	0.00	4.26
728	891	1.272490	CTAGAGGTGTTGGTCGAGCAA	59.728	52.381	25.16	25.16	0.00	3.91
729	892	0.034059	AGAGGTGTTGGTCGAGCAAG	59.966	55.000	28.94	0.00	0.00	4.01
730	893	1.569479	GAGGTGTTGGTCGAGCAAGC	61.569	60.000	28.94	22.70	0.00	4.01
731	894	1.891919	GGTGTTGGTCGAGCAAGCA	60.892	57.895	28.94	24.11	0.00	3.91
732	895	1.279840	GTGTTGGTCGAGCAAGCAC	59.720	57.895	28.94	29.13	0.00	4.40
733	896	1.153269	TGTTGGTCGAGCAAGCACA	60.153	52.632	28.94	21.37	0.00	4.57
734	897	0.746204	TGTTGGTCGAGCAAGCACAA	60.746	50.000	28.94	10.73	0.00	3.33
735	898	0.040958	GTTGGTCGAGCAAGCACAAG	60.041	55.000	28.94	0.00	0.00	3.16
736	899	0.463654	TTGGTCGAGCAAGCACAAGT	60.464	50.000	25.16	0.00	0.00	3.16
737	900	1.159713	TGGTCGAGCAAGCACAAGTG	61.160	55.000	16.20	0.00	0.00	3.16
749	912	1.800805	CACAAGTGCTAGAGGTGGTG	58.199	55.000	0.00	0.00	0.00	4.17
750	913	0.687354	ACAAGTGCTAGAGGTGGTGG	59.313	55.000	0.00	0.00	0.00	4.61
751	914	0.687354	CAAGTGCTAGAGGTGGTGGT	59.313	55.000	0.00	0.00	0.00	4.16
851	1086	5.687441	CGGAGAGGAATGGTTGATAATGGAA	60.687	44.000	0.00	0.00	0.00	3.53
1012	1252	0.918258	TGTAGGCATGGCTTCATCCA	59.082	50.000	28.30	13.14	40.97	3.41
1016	1256	1.188863	GGCATGGCTTCATCCAGTTT	58.811	50.000	12.86	0.00	39.89	2.66
1252	1492	5.700832	CCAACTAACGCATATGACATACCAT	59.299	40.000	6.97	0.00	0.00	3.55
1341	1581	3.767673	ACTTTTATGTAGTCGCCTCCTCA	59.232	43.478	0.00	0.00	0.00	3.86
1390	1630	4.345859	TCACGAGGTACCAAAAGATGTT	57.654	40.909	15.94	0.00	0.00	2.71
1493	1733	3.637229	TCGTGAGAAGGAGAAGAACAAGT	59.363	43.478	0.00	0.00	37.03	3.16
1528	1768	0.326264	AAGAGAGGGCACGCAAAGAT	59.674	50.000	0.00	0.00	0.00	2.40
1657	1898	2.380064	AGACAAATGGAAAGGCACCA	57.620	45.000	0.00	0.00	41.83	4.17
1722	1986	0.955905	TCATTCGAGACCGTGTGTGA	59.044	50.000	0.00	0.00	37.05	3.58
2022	3179	1.987855	CCAAGGTCCCTGGCGTCTA	60.988	63.158	0.00	0.00	0.00	2.59
2023	3180	1.338136	CCAAGGTCCCTGGCGTCTAT	61.338	60.000	0.00	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
11	12	1.334869	CCGTGAAGACTTGCTTGCTTT	59.665	47.619	0.00	0.00	36.83	3.51
51	52	9.234384	CAATTTGATAGATCATTTCAGTTCTGC	57.766	33.333	0.00	0.00	36.56	4.26
310	311	2.229784	CTGTGATTGGTCCAAGAAAGGC	59.770	50.000	10.72	0.00	0.00	4.35
504	505	2.034066	CTTCACCGCACACCCCAT	59.966	61.111	0.00	0.00	0.00	4.00
717	880	0.463654	ACTTGTGCTTGCTCGACCAA	60.464	50.000	0.00	0.00	0.00	3.67
723	886	1.731160	CTCTAGCACTTGTGCTTGCTC	59.269	52.381	29.37	0.08	46.31	4.26
725	888	0.801251	CCTCTAGCACTTGTGCTTGC	59.199	55.000	29.37	3.78	43.52	4.01
726	889	1.802960	CACCTCTAGCACTTGTGCTTG	59.197	52.381	29.37	26.37	43.52	4.01
727	890	1.271054	CCACCTCTAGCACTTGTGCTT	60.271	52.381	29.37	15.68	43.52	3.91
729	892	0.035458	ACCACCTCTAGCACTTGTGC	59.965	55.000	16.98	16.98	0.00	4.57
730	893	1.609061	CCACCACCTCTAGCACTTGTG	60.609	57.143	0.00	0.00	0.00	3.33
731	894	0.687354	CCACCACCTCTAGCACTTGT	59.313	55.000	0.00	0.00	0.00	3.16
732	895	0.687354	ACCACCACCTCTAGCACTTG	59.313	55.000	0.00	0.00	0.00	3.16
733	896	0.687354	CACCACCACCTCTAGCACTT	59.313	55.000	0.00	0.00	0.00	3.16
734	897	1.194781	CCACCACCACCTCTAGCACT	61.195	60.000	0.00	0.00	0.00	4.40
735	898	1.296715	CCACCACCACCTCTAGCAC	59.703	63.158	0.00	0.00	0.00	4.40
736	899	1.152118	ACCACCACCACCTCTAGCA	60.152	57.895	0.00	0.00	0.00	3.49
737	900	1.597461	GACCACCACCACCTCTAGC	59.403	63.158	0.00	0.00	0.00	3.42
738	901	0.611062	TCGACCACCACCACCTCTAG	60.611	60.000	0.00	0.00	0.00	2.43
739	902	0.178955	TTCGACCACCACCACCTCTA	60.179	55.000	0.00	0.00	0.00	2.43
740	903	1.458777	TTCGACCACCACCACCTCT	60.459	57.895	0.00	0.00	0.00	3.69
741	904	1.004918	CTTCGACCACCACCACCTC	60.005	63.158	0.00	0.00	0.00	3.85
742	905	1.458777	TCTTCGACCACCACCACCT	60.459	57.895	0.00	0.00	0.00	4.00
743	906	1.004918	CTCTTCGACCACCACCACC	60.005	63.158	0.00	0.00	0.00	4.61
744	907	1.004918	CCTCTTCGACCACCACCAC	60.005	63.158	0.00	0.00	0.00	4.16
745	908	0.761323	TTCCTCTTCGACCACCACCA	60.761	55.000	0.00	0.00	0.00	4.17
746	909	0.037232	CTTCCTCTTCGACCACCACC	60.037	60.000	0.00	0.00	0.00	4.61
747	910	0.670854	GCTTCCTCTTCGACCACCAC	60.671	60.000	0.00	0.00	0.00	4.16
748	911	1.118965	TGCTTCCTCTTCGACCACCA	61.119	55.000	0.00	0.00	0.00	4.17
749	912	0.670854	GTGCTTCCTCTTCGACCACC	60.671	60.000	0.00	0.00	0.00	4.61
750	913	0.033504	TGTGCTTCCTCTTCGACCAC	59.966	55.000	0.00	0.00	0.00	4.16
751	914	0.756294	TTGTGCTTCCTCTTCGACCA	59.244	50.000	0.00	0.00	0.00	4.02
1012	1252	2.657237	CGGCCTCGTCCTGAAACT	59.343	61.111	0.00	0.00	0.00	2.66
1033	1273	4.070552	GTCCTCTTGGTCCGCGCT	62.071	66.667	5.56	0.00	34.23	5.92
1390	1630	2.525368	TCTCGATGTTGGTCCTCTTGA	58.475	47.619	0.00	0.00	0.00	3.02
1493	1733	0.532640	TCTTGCTCACGCTTCTTGCA	60.533	50.000	0.00	0.00	43.06	4.08
1528	1768	2.755655	CTCTTCTTGACGAGCCTCCTTA	59.244	50.000	0.00	0.00	0.00	2.69
1572	1812	2.026734	CCTCTCGTGCATCGCGAT	59.973	61.111	17.62	17.62	45.17	4.58
1657	1898	2.488153	TCGATATTCCATCATCGACGCT	59.512	45.455	2.76	0.00	45.85	5.07
1841	2203	8.313292	ACATAATTTCAAATAGGTTGCACACAT	58.687	29.630	0.00	0.00	37.13	3.21
1970	3122	1.770658	CTGGTCTGGATATGGAGCCAA	59.229	52.381	0.00	0.00	41.72	4.52
2022	3179	1.148310	CTGCGTGACCAAAACGAGAT	58.852	50.000	0.00	0.00	43.68	2.75
2023	3180	0.878523	CCTGCGTGACCAAAACGAGA	60.879	55.000	0.00	0.00	43.68	4.04
2060	3217	2.094545	GCGTCTGGCTTTTTGGATGATT	60.095	45.455	0.00	0.00	39.11	2.57
2069	3226	1.150536	TCCTTGGCGTCTGGCTTTT	59.849	52.632	0.00	0.00	42.94	2.27
2144	3476	2.251642	AAAACGAGCCAGACGCCAC	61.252	57.895	0.00	0.00	38.78	5.01
2171	3503	2.035632	CAGATAGGTGTCTGGTCTCCC	58.964	57.143	0.00	0.00	41.49	4.30
2187	3519	2.901192	CTGGCTCTCTGGATGATCAGAT	59.099	50.000	0.09	0.00	42.19	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.