AutoCloner

Multiple sequence alignment - TraesCS2D01G092300

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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	TraesCS2D01G092300	chr2D	100.000	2669	0	0	1	2669	43963090	43965758	0.000000e+00	4929.0
1	TraesCS2D01G092300	chr2D	98.007	903	15	2	1770	2669	2672219	2673121	0.000000e+00	1565.0
2	TraesCS2D01G092300	chr2D	97.010	903	22	3	1769	2669	298499860	298500759	0.000000e+00	1513.0
3	TraesCS2D01G092300	chr2D	87.068	897	57	27	853	1738	43951977	43952825	0.000000e+00	959.0
4	TraesCS2D01G092300	chr2D	92.308	65	5	0	772	836	43951817	43951881	2.830000e-15	93.5
5	TraesCS2D01G092300	chr5D	97.901	905	15	1	1769	2669	449899580	449898676	0.000000e+00	1563.0
6	TraesCS2D01G092300	chr1D	97.003	901	25	2	1769	2669	108803737	108802839	0.000000e+00	1513.0
7	TraesCS2D01G092300	chr1D	95.365	863	19	1	1807	2669	18200050	18199209	0.000000e+00	1352.0
8	TraesCS2D01G092300	chr7D	96.788	903	27	1	1769	2669	71351283	71352185	0.000000e+00	1506.0
9	TraesCS2D01G092300	chr7D	86.247	429	41	9	980	1398	3540012	3539592	1.460000e-122	449.0
10	TraesCS2D01G092300	chrUn	96.392	887	23	1	1783	2669	111030147	111029270	0.000000e+00	1452.0
11	TraesCS2D01G092300	chr7A	89.525	926	68	15	1769	2667	112959043	112959966	0.000000e+00	1146.0
12	TraesCS2D01G092300	chr6A	91.500	800	53	12	1771	2566	107842650	107843438	0.000000e+00	1086.0
13	TraesCS2D01G092300	chr2A	87.293	905	47	18	853	1750	47673159	47674002	0.000000e+00	972.0
14	TraesCS2D01G092300	chr2A	93.162	234	9	4	605	836	47666986	47667214	1.180000e-88	337.0
15	TraesCS2D01G092300	chr2A	84.127	315	26	18	176	489	47666685	47666976	1.560000e-72	283.0
16	TraesCS2D01G092300	chr2A	84.000	150	15	5	1	148	47666467	47666609	4.630000e-28	135.0
17	TraesCS2D01G092300	chr2B	89.986	699	35	15	853	1543	68756472	68757143	0.000000e+00	870.0
18	TraesCS2D01G092300	chr2B	85.448	859	61	24	20	836	68586590	68585754	0.000000e+00	835.0
19	TraesCS2D01G092300	chr2B	83.608	909	64	33	853	1750	68585670	68584836	0.000000e+00	774.0
20	TraesCS2D01G092300	chr2B	88.245	604	34	19	1159	1738	68722568	68723158	0.000000e+00	688.0
21	TraesCS2D01G092300	chr2B	89.403	519	33	7	333	836	68791622	68792133	3.750000e-178	634.0
22	TraesCS2D01G092300	chr2B	91.443	409	30	3	397	804	68722157	68722561	8.350000e-155	556.0
23	TraesCS2D01G092300	chr2B	92.458	358	18	6	1383	1737	68816661	68817012	1.100000e-138	503.0
24	TraesCS2D01G092300	chr2B	93.238	281	11	3	1	277	68789591	68789867	8.900000e-110	407.0
25	TraesCS2D01G092300	chr2B	92.884	267	13	3	1	266	68705964	68706225	1.500000e-102	383.0
26	TraesCS2D01G092300	chr2B	88.424	311	23	7	1	302	68736463	68736769	1.950000e-96	363.0
27	TraesCS2D01G092300	chr2B	95.580	181	6	1	1558	1738	68757260	68757438	3.360000e-74	289.0
28	TraesCS2D01G092300	chr2B	89.316	234	19	2	1092	1322	68816246	68816476	3.360000e-74	289.0
29	TraesCS2D01G092300	chr2B	92.969	128	8	1	968	1094	68792943	68793070	4.540000e-43	185.0
30	TraesCS2D01G092300	chr2B	87.671	73	9	0	1448	1520	678088506	678088434	4.730000e-13	86.1
31	TraesCS2D01G092300	chr2B	84.043	94	5	2	854	947	68792859	68792942	6.120000e-12	82.4
32	TraesCS2D01G092300	chr6D	89.855	69	7	0	1448	1516	106049381	106049449	3.660000e-14	89.8
33	TraesCS2D01G092300	chr6B	89.855	69	7	0	1448	1516	192738723	192738791	3.660000e-14	89.8
34	TraesCS2D01G092300	chr4A	86.250	80	7	1	980	1055	739694564	739694643	1.700000e-12	84.2
35	TraesCS2D01G092300	chr4A	86.250	80	7	1	980	1055	742088572	742088651	1.700000e-12	84.2

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	TraesCS2D01G092300	chr2D	43963090	43965758	2668	False	4929.000000	4929	100.000000	1	2669	1	chr2D.!!$F2	2668
1	TraesCS2D01G092300	chr2D	2672219	2673121	902	False	1565.000000	1565	98.007000	1770	2669	1	chr2D.!!$F1	899
2	TraesCS2D01G092300	chr2D	298499860	298500759	899	False	1513.000000	1513	97.010000	1769	2669	1	chr2D.!!$F3	900
3	TraesCS2D01G092300	chr2D	43951817	43952825	1008	False	526.250000	959	89.688000	772	1738	2	chr2D.!!$F4	966
4	TraesCS2D01G092300	chr5D	449898676	449899580	904	True	1563.000000	1563	97.901000	1769	2669	1	chr5D.!!$R1	900
5	TraesCS2D01G092300	chr1D	108802839	108803737	898	True	1513.000000	1513	97.003000	1769	2669	1	chr1D.!!$R2	900
6	TraesCS2D01G092300	chr1D	18199209	18200050	841	True	1352.000000	1352	95.365000	1807	2669	1	chr1D.!!$R1	862
7	TraesCS2D01G092300	chr7D	71351283	71352185	902	False	1506.000000	1506	96.788000	1769	2669	1	chr7D.!!$F1	900
8	TraesCS2D01G092300	chrUn	111029270	111030147	877	True	1452.000000	1452	96.392000	1783	2669	1	chrUn.!!$R1	886
9	TraesCS2D01G092300	chr7A	112959043	112959966	923	False	1146.000000	1146	89.525000	1769	2667	1	chr7A.!!$F1	898
10	TraesCS2D01G092300	chr6A	107842650	107843438	788	False	1086.000000	1086	91.500000	1771	2566	1	chr6A.!!$F1	795
11	TraesCS2D01G092300	chr2A	47673159	47674002	843	False	972.000000	972	87.293000	853	1750	1	chr2A.!!$F1	897
12	TraesCS2D01G092300	chr2A	47666467	47667214	747	False	251.666667	337	87.096333	1	836	3	chr2A.!!$F2	835
13	TraesCS2D01G092300	chr2B	68584836	68586590	1754	True	804.500000	835	84.528000	20	1750	2	chr2B.!!$R2	1730
14	TraesCS2D01G092300	chr2B	68722157	68723158	1001	False	622.000000	688	89.844000	397	1738	2	chr2B.!!$F3	1341
15	TraesCS2D01G092300	chr2B	68756472	68757438	966	False	579.500000	870	92.783000	853	1738	2	chr2B.!!$F4	885
16	TraesCS2D01G092300	chr2B	68816246	68817012	766	False	396.000000	503	90.887000	1092	1737	2	chr2B.!!$F6	645
17	TraesCS2D01G092300	chr2B	68789591	68793070	3479	False	327.100000	634	89.913250	1	1094	4	chr2B.!!$F5	1093

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
892	3450	0.518559	GCGATCGCGTTTCTGTTTCC	60.519	55.0	26.12	0.0	40.36	3.13	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1758	4597	0.249911	GCCGCGGGAGATTGTCTTAT	60.25	55.0	29.38	0.0	0.0	1.73	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
35	36	5.116069	ACGGTGCAAGAAAATCGTATTTT	57.884	34.783	0.00	5.59	0.00	1.82
36	37	5.525199	ACGGTGCAAGAAAATCGTATTTTT	58.475	33.333	0.00	1.55	0.00	1.94
316	2049	2.052157	GGCTTCGTACATATCAGACGC	58.948	52.381	0.00	0.00	36.54	5.19
361	2135	4.789807	CTGGGATTCCACATCTTCAGAAT	58.210	43.478	4.80	0.00	38.32	2.40
394	2168	3.657727	TGAAAGGGAGGGTTCTTGAAGAT	59.342	43.478	0.00	0.00	0.00	2.40
395	2169	4.263506	TGAAAGGGAGGGTTCTTGAAGATC	60.264	45.833	0.00	0.00	0.00	2.75
402	2176	2.420687	GGGTTCTTGAAGATCGAGGCAT	60.421	50.000	0.00	0.00	0.00	4.40
489	2263	1.517832	CCCTGAAGCCAGTAGACGG	59.482	63.158	0.00	0.00	38.74	4.79
490	2264	0.970937	CCCTGAAGCCAGTAGACGGA	60.971	60.000	0.00	0.00	38.74	4.69
494	2268	2.688446	CTGAAGCCAGTAGACGGACATA	59.312	50.000	0.00	0.00	35.70	2.29
495	2269	3.093814	TGAAGCCAGTAGACGGACATAA	58.906	45.455	0.00	0.00	0.00	1.90
496	2270	3.704566	TGAAGCCAGTAGACGGACATAAT	59.295	43.478	0.00	0.00	0.00	1.28
497	2271	4.891168	TGAAGCCAGTAGACGGACATAATA	59.109	41.667	0.00	0.00	0.00	0.98
600	2381	0.672711	CATGATCGCGATGATGCCCT	60.673	55.000	30.50	4.84	37.47	5.19
634	2415	3.838271	GCCGCCGATGGAGTCTGA	61.838	66.667	0.00	0.00	0.00	3.27
636	2417	2.418910	CCGCCGATGGAGTCTGAGT	61.419	63.158	0.00	0.00	0.00	3.41
807	2594	2.655364	CAGCACGAGCCGATACCG	60.655	66.667	0.00	0.00	43.56	4.02
827	2621	4.776322	CTCCACGATGCGGCCCAA	62.776	66.667	0.00	0.00	0.00	4.12
845	3398	1.265905	CAAGGCAAGGTTCACGTTACC	59.734	52.381	8.28	8.28	35.85	2.85
846	3399	0.601841	AGGCAAGGTTCACGTTACCG	60.602	55.000	10.18	0.49	40.69	4.02
892	3450	0.518559	GCGATCGCGTTTCTGTTTCC	60.519	55.000	26.12	0.00	40.36	3.13
896	3454	2.254350	GCGTTTCTGTTTCCGGCC	59.746	61.111	0.00	0.00	0.00	6.13
897	3455	2.554272	CGTTTCTGTTTCCGGCCG	59.446	61.111	21.04	21.04	0.00	6.13
898	3456	2.254350	GTTTCTGTTTCCGGCCGC	59.746	61.111	22.85	6.58	0.00	6.53
899	3457	3.350612	TTTCTGTTTCCGGCCGCG	61.351	61.111	22.85	13.93	0.00	6.46
958	3516	2.820037	GCGCTGAGCTTACCCCAC	60.820	66.667	1.78	0.00	44.04	4.61
959	3517	2.509336	CGCTGAGCTTACCCCACG	60.509	66.667	1.78	0.00	0.00	4.94
960	3518	2.663196	GCTGAGCTTACCCCACGT	59.337	61.111	0.00	0.00	0.00	4.49
961	3519	1.448013	GCTGAGCTTACCCCACGTC	60.448	63.158	0.00	0.00	0.00	4.34
962	3520	1.218316	CTGAGCTTACCCCACGTCC	59.782	63.158	0.00	0.00	0.00	4.79
990	3549	3.216292	GCACCAACGCCAACCACT	61.216	61.111	0.00	0.00	0.00	4.00
1012	3574	1.469767	CCACGACGATGCAGATCTTCA	60.470	52.381	0.00	0.00	29.23	3.02
1104	3666	0.620556	GGATCCAGGACAAGCAAGGA	59.379	55.000	6.95	0.00	0.00	3.36
1173	3735	4.760047	TTCGCCGGGAAGCAGCTC	62.760	66.667	2.18	0.00	0.00	4.09
1182	3747	1.515304	GAAGCAGCTCGACGAGGAC	60.515	63.158	25.31	10.43	0.00	3.85
1358	4049	0.665068	TGCCGCAAGTACGTACACAG	60.665	55.000	26.55	16.21	0.00	3.66
1363	4054	1.712350	GCAAGTACGTACACAGACACG	59.288	52.381	26.55	7.28	43.63	4.49
1373	4064	4.212847	CGTACACAGACACGCCTATAGTAT	59.787	45.833	0.00	0.00	0.00	2.12
1374	4065	5.406477	CGTACACAGACACGCCTATAGTATA	59.594	44.000	0.00	0.00	0.00	1.47
1375	4066	5.686159	ACACAGACACGCCTATAGTATAC	57.314	43.478	0.00	0.00	0.00	1.47
1381	4087	8.316946	ACAGACACGCCTATAGTATACTACATA	58.683	37.037	14.82	5.12	0.00	2.29
1431	4139	4.612412	TTTTCTCCGGCCGCACGT	62.612	61.111	22.85	0.00	0.00	4.49
1593	4416	1.849097	CCAATAACGTCCTACCTCGC	58.151	55.000	0.00	0.00	0.00	5.03
1750	4589	0.733150	CTGCACCAGTGATCAGCATG	59.267	55.000	7.00	1.88	34.35	4.06
1751	4590	3.999915	TCTGCACCAGTGATCAGCATGA	62.000	50.000	7.00	5.00	40.46	3.07
2583	5449	1.235112	GTTCGGAGGGGGATAGGGA	59.765	63.158	0.00	0.00	0.00	4.20

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
361	2135	2.342406	TCCCTTTCATCAGGAGACCA	57.658	50.000	0.00	0.00	35.71	4.02
441	2215	0.941542	GCCAACTGCTCGTACAACAA	59.058	50.000	0.00	0.00	36.87	2.83
489	2263	6.367969	AGTTGTGGTTTGACGACTATTATGTC	59.632	38.462	0.00	0.00	38.58	3.06
490	2264	6.228258	AGTTGTGGTTTGACGACTATTATGT	58.772	36.000	0.00	0.00	38.58	2.29
494	2268	3.739300	CGAGTTGTGGTTTGACGACTATT	59.261	43.478	0.00	0.00	40.16	1.73
495	2269	3.243636	ACGAGTTGTGGTTTGACGACTAT	60.244	43.478	0.00	0.00	40.16	2.12
496	2270	2.099592	ACGAGTTGTGGTTTGACGACTA	59.900	45.455	0.00	0.00	40.16	2.59
497	2271	1.134907	ACGAGTTGTGGTTTGACGACT	60.135	47.619	0.00	0.00	42.35	4.18
525	2299	4.758251	CAGGTGTCCATGGCGCGA	62.758	66.667	12.10	0.00	0.00	5.87
621	2402	0.457851	GGTCACTCAGACTCCATCGG	59.542	60.000	0.00	0.00	46.72	4.18
622	2403	0.457851	GGGTCACTCAGACTCCATCG	59.542	60.000	0.00	0.00	46.72	3.84
624	2405	1.608717	GCGGGTCACTCAGACTCCAT	61.609	60.000	0.00	0.00	45.38	3.41
625	2406	2.276116	GCGGGTCACTCAGACTCCA	61.276	63.158	0.00	0.00	45.38	3.86
627	2408	1.303799	TACGCGGGTCACTCAGACTC	61.304	60.000	12.47	0.00	46.72	3.36
628	2409	1.303074	TACGCGGGTCACTCAGACT	60.303	57.895	12.47	0.00	46.72	3.24
629	2410	1.136984	CTACGCGGGTCACTCAGAC	59.863	63.158	12.47	0.00	46.83	3.51
630	2411	2.044555	CCTACGCGGGTCACTCAGA	61.045	63.158	12.47	0.00	0.00	3.27
631	2412	1.994507	CTCCTACGCGGGTCACTCAG	61.995	65.000	12.47	0.00	0.00	3.35
634	2415	2.754658	CCTCCTACGCGGGTCACT	60.755	66.667	12.47	0.00	0.00	3.41
749	2536	0.841961	AGCCATGCATGCTCTCCTAA	59.158	50.000	21.69	0.00	32.41	2.69
827	2621	3.317449	GGTAACGTGAACCTTGCCT	57.683	52.632	12.05	0.00	33.97	4.75
846	3399	4.468689	GAGTAGCCCACGCCCCAC	62.469	72.222	0.00	0.00	34.57	4.61
850	3403	3.600898	AAACCGAGTAGCCCACGCC	62.601	63.158	0.00	0.00	34.57	5.68
851	3404	2.047560	AAACCGAGTAGCCCACGC	60.048	61.111	0.00	0.00	0.00	5.34
985	3544	1.214589	GCATCGTCGTGGTAGTGGT	59.785	57.895	0.00	0.00	0.00	4.16
990	3549	1.389555	AGATCTGCATCGTCGTGGTA	58.610	50.000	0.00	0.00	33.75	3.25
1012	3574	1.224592	GCCCGGTGATGGTCTTGAT	59.775	57.895	0.00	0.00	0.00	2.57
1059	3621	3.185082	GACGGTGTCGACGGTGTCA	62.185	63.158	21.62	0.00	35.88	3.58
1358	4049	8.715191	AGTATGTAGTATACTATAGGCGTGTC	57.285	38.462	15.53	0.82	43.54	3.67
1395	4101	8.221251	GGAGAAAACCTAATTAGGATGGAGATT	58.779	37.037	33.60	15.26	46.63	2.40
1402	4110	4.445879	GGCCGGAGAAAACCTAATTAGGAT	60.446	45.833	33.60	21.94	46.63	3.24
1412	4120	3.733960	GTGCGGCCGGAGAAAACC	61.734	66.667	29.38	7.18	0.00	3.27
1431	4139	5.890985	CACCTGTAAATGAATCAATGGGGTA	59.109	40.000	0.00	0.00	0.00	3.69
1750	4589	5.220681	GCGGGAGATTGTCTTATTTTCAGTC	60.221	44.000	0.00	0.00	0.00	3.51
1751	4590	4.636206	GCGGGAGATTGTCTTATTTTCAGT	59.364	41.667	0.00	0.00	0.00	3.41
1752	4591	4.260375	CGCGGGAGATTGTCTTATTTTCAG	60.260	45.833	0.00	0.00	0.00	3.02
1753	4592	3.621268	CGCGGGAGATTGTCTTATTTTCA	59.379	43.478	0.00	0.00	0.00	2.69
1754	4593	3.002348	CCGCGGGAGATTGTCTTATTTTC	59.998	47.826	20.10	0.00	0.00	2.29
1755	4594	2.943033	CCGCGGGAGATTGTCTTATTTT	59.057	45.455	20.10	0.00	0.00	1.82
1756	4595	2.561569	CCGCGGGAGATTGTCTTATTT	58.438	47.619	20.10	0.00	0.00	1.40
1757	4596	1.810412	GCCGCGGGAGATTGTCTTATT	60.810	52.381	29.38	0.00	0.00	1.40
1758	4597	0.249911	GCCGCGGGAGATTGTCTTAT	60.250	55.000	29.38	0.00	0.00	1.73
1759	4598	1.143183	GCCGCGGGAGATTGTCTTA	59.857	57.895	29.38	0.00	0.00	2.10
1760	4599	2.125106	GCCGCGGGAGATTGTCTT	60.125	61.111	29.38	0.00	0.00	3.01
1761	4600	3.077556	AGCCGCGGGAGATTGTCT	61.078	61.111	29.38	9.81	0.00	3.41
1762	4601	2.586357	GAGCCGCGGGAGATTGTC	60.586	66.667	29.38	7.21	0.00	3.18
1763	4602	4.162690	GGAGCCGCGGGAGATTGT	62.163	66.667	29.38	0.00	0.00	2.71
1764	4603	4.918201	GGGAGCCGCGGGAGATTG	62.918	72.222	29.38	0.00	0.00	2.67
2070	4909	3.254024	AAGAAGCCCACGCCACGAT	62.254	57.895	0.00	0.00	34.57	3.73
2146	4985	2.677199	GAAGCAACAGATCTGACACGA	58.323	47.619	29.27	0.00	0.00	4.35

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.