AutoCloner

Multiple sequence alignment - TraesCS2D01G044500

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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	TraesCS2D01G044500	chr2D	100.000	2547	0	0	1	2547	16064869	16067415	0.000000e+00	4704
1	TraesCS2D01G044500	chr7D	95.141	1955	61	10	618	2547	94497477	94495532	0.000000e+00	3053
2	TraesCS2D01G044500	chr4D	94.882	1954	67	13	618	2547	459886443	459884499	0.000000e+00	3024
3	TraesCS2D01G044500	chr4D	95.116	1679	60	13	882	2547	43272457	43270788	0.000000e+00	2627
4	TraesCS2D01G044500	chr3B	94.241	1962	75	10	616	2547	599079413	599077460	0.000000e+00	2963
5	TraesCS2D01G044500	chr3A	94.321	1937	93	12	617	2547	164803400	164801475	0.000000e+00	2952
6	TraesCS2D01G044500	chr4A	94.070	1956	85	9	618	2547	724524709	724522759	0.000000e+00	2940
7	TraesCS2D01G044500	chr1B	93.292	1953	95	11	618	2547	641549866	641547927	0.000000e+00	2848
8	TraesCS2D01G044500	chr5B	95.590	1610	59	7	938	2541	452113014	452111411	0.000000e+00	2569
9	TraesCS2D01G044500	chr5B	90.041	492	36	8	618	1097	18695162	18694672	2.150000e-175	625
10	TraesCS2D01G044500	chr5B	88.732	142	4	1	41	170	330622422	330622563	2.030000e-36	163
11	TraesCS2D01G044500	chr6D	93.482	1703	86	11	618	2302	329896761	329895066	0.000000e+00	2507
12	TraesCS2D01G044500	chr7A	91.319	576	32	5	1	570	431251622	431251059	0.000000e+00	771
13	TraesCS2D01G044500	chr7A	88.732	142	4	1	41	170	621577469	621577328	2.030000e-36	163
14	TraesCS2D01G044500	chr2A	97.183	355	9	1	618	971	233255261	233255615	1.300000e-167	599
15	TraesCS2D01G044500	chr2A	95.028	362	14	3	614	971	611725141	611724780	1.320000e-157	566
16	TraesCS2D01G044500	chr1D	96.369	358	9	1	618	971	17040736	17040379	1.020000e-163	586
17	TraesCS2D01G044500	chr6A	95.833	360	14	1	613	971	57901154	57901513	4.720000e-162	580
18	TraesCS2D01G044500	chr6B	88.732	142	4	1	41	170	184798927	184798786	2.030000e-36	163
19	TraesCS2D01G044500	chr2B	88.028	142	5	1	41	170	33816065	33816206	9.430000e-35	158

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	TraesCS2D01G044500	chr2D	16064869	16067415	2546	False	4704	4704	100.000	1	2547	1	chr2D.!!$F1	2546
1	TraesCS2D01G044500	chr7D	94495532	94497477	1945	True	3053	3053	95.141	618	2547	1	chr7D.!!$R1	1929
2	TraesCS2D01G044500	chr4D	459884499	459886443	1944	True	3024	3024	94.882	618	2547	1	chr4D.!!$R2	1929
3	TraesCS2D01G044500	chr4D	43270788	43272457	1669	True	2627	2627	95.116	882	2547	1	chr4D.!!$R1	1665
4	TraesCS2D01G044500	chr3B	599077460	599079413	1953	True	2963	2963	94.241	616	2547	1	chr3B.!!$R1	1931
5	TraesCS2D01G044500	chr3A	164801475	164803400	1925	True	2952	2952	94.321	617	2547	1	chr3A.!!$R1	1930
6	TraesCS2D01G044500	chr4A	724522759	724524709	1950	True	2940	2940	94.070	618	2547	1	chr4A.!!$R1	1929
7	TraesCS2D01G044500	chr1B	641547927	641549866	1939	True	2848	2848	93.292	618	2547	1	chr1B.!!$R1	1929
8	TraesCS2D01G044500	chr5B	452111411	452113014	1603	True	2569	2569	95.590	938	2541	1	chr5B.!!$R2	1603
9	TraesCS2D01G044500	chr6D	329895066	329896761	1695	True	2507	2507	93.482	618	2302	1	chr6D.!!$R1	1684
10	TraesCS2D01G044500	chr7A	431251059	431251622	563	True	771	771	91.319	1	570	1	chr7A.!!$R1	569

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
579	586	0.17668	CAGGGCAGATTAGCACGAGT	59.823	55.0	0.0	0.0	44.43	4.18	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2223	2332	1.480545	TCCTAGCAGTTATCAGCGCAA	59.519	47.619	11.47	0.0	35.48	4.85	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
41	42	6.128090	GCTTAAGCAAATAAAAGGTACGAGGT	60.128	38.462	22.59	0.00	41.59	3.85
48	49	9.480053	GCAAATAAAAGGTACGAGGTATGTATA	57.520	33.333	0.00	0.00	0.00	1.47
72	73	3.068560	CCACCAAATCCAACATTTGCAG	58.931	45.455	2.12	0.00	37.60	4.41
135	136	0.749454	GCTGGTGCAGGGGTTATCAG	60.749	60.000	0.00	0.00	39.41	2.90
149	150	4.184629	GGTTATCAGCTACTCCAGTGTTG	58.815	47.826	0.00	0.00	0.00	3.33
164	165	4.440525	CCAGTGTTGTCATGTTTCTTGCTT	60.441	41.667	0.00	0.00	0.00	3.91
252	253	3.756434	TCTGGAAACCGAAATAAGCTTGG	59.244	43.478	9.86	3.44	0.00	3.61
253	254	3.756434	CTGGAAACCGAAATAAGCTTGGA	59.244	43.478	9.86	0.00	0.00	3.53
264	265	8.552034	CCGAAATAAGCTTGGAAAATCTACTAG	58.448	37.037	9.86	0.00	0.00	2.57
266	267	7.809546	AATAAGCTTGGAAAATCTACTAGCC	57.190	36.000	9.86	0.00	0.00	3.93
401	402	6.737254	TTTAGACAAGAAATCGATGGGAAC	57.263	37.500	0.00	0.00	0.00	3.62
449	450	3.092511	ATCTGGTGGGGCGCTCAT	61.093	61.111	10.74	0.00	0.00	2.90
451	452	3.790437	CTGGTGGGGCGCTCATCT	61.790	66.667	10.74	0.00	0.00	2.90
454	455	2.821366	GTGGGGCGCTCATCTGTG	60.821	66.667	10.74	0.00	0.00	3.66
460	461	1.160137	GGCGCTCATCTGTGAAGTTT	58.840	50.000	7.64	0.00	33.05	2.66
465	466	3.970610	CGCTCATCTGTGAAGTTTTGTTG	59.029	43.478	0.00	0.00	33.05	3.33
466	467	4.496341	CGCTCATCTGTGAAGTTTTGTTGT	60.496	41.667	0.00	0.00	33.05	3.32
467	468	4.736793	GCTCATCTGTGAAGTTTTGTTGTG	59.263	41.667	0.00	0.00	33.05	3.33
573	580	2.592861	CCGGCAGGGCAGATTAGC	60.593	66.667	0.00	0.00	0.00	3.09
574	581	2.190313	CGGCAGGGCAGATTAGCA	59.810	61.111	0.00	0.00	35.83	3.49
575	582	2.182842	CGGCAGGGCAGATTAGCAC	61.183	63.158	0.00	0.00	38.51	4.40
576	583	2.182842	GGCAGGGCAGATTAGCACG	61.183	63.158	0.00	0.00	44.43	5.34
577	584	1.153369	GCAGGGCAGATTAGCACGA	60.153	57.895	0.00	0.00	44.43	4.35
578	585	1.156645	GCAGGGCAGATTAGCACGAG	61.157	60.000	0.00	0.00	44.43	4.18
579	586	0.176680	CAGGGCAGATTAGCACGAGT	59.823	55.000	0.00	0.00	44.43	4.18
580	587	0.176680	AGGGCAGATTAGCACGAGTG	59.823	55.000	0.00	0.00	44.43	3.51
581	588	0.811616	GGGCAGATTAGCACGAGTGG	60.812	60.000	5.32	0.00	35.83	4.00
582	589	1.432270	GGCAGATTAGCACGAGTGGC	61.432	60.000	5.32	0.00	35.83	5.01
584	591	1.141881	AGATTAGCACGAGTGGCGG	59.858	57.895	5.32	0.00	46.49	6.13
585	592	2.511600	ATTAGCACGAGTGGCGGC	60.512	61.111	0.00	0.00	46.49	6.53
607	614	2.805546	GCGTAGTCGAGCCCATCA	59.194	61.111	0.00	0.00	39.71	3.07
608	615	1.141019	GCGTAGTCGAGCCCATCAA	59.859	57.895	0.00	0.00	39.71	2.57
609	616	0.249489	GCGTAGTCGAGCCCATCAAT	60.249	55.000	0.00	0.00	39.71	2.57
610	617	1.806623	GCGTAGTCGAGCCCATCAATT	60.807	52.381	0.00	0.00	39.71	2.32
611	618	2.128035	CGTAGTCGAGCCCATCAATTC	58.872	52.381	0.00	0.00	39.71	2.17
612	619	2.481276	CGTAGTCGAGCCCATCAATTCA	60.481	50.000	0.00	0.00	39.71	2.57
613	620	2.787473	AGTCGAGCCCATCAATTCAA	57.213	45.000	0.00	0.00	0.00	2.69
614	621	3.071874	AGTCGAGCCCATCAATTCAAA	57.928	42.857	0.00	0.00	0.00	2.69
686	693	1.741706	CCTCAGATGCGAATTGTGCTT	59.258	47.619	0.00	0.00	0.00	3.91
782	792	1.571773	GCCCTTACAGGTGGGACCAT	61.572	60.000	1.75	0.00	46.15	3.55
785	795	0.327924	CTTACAGGTGGGACCATGCA	59.672	55.000	0.00	0.00	41.95	3.96
1324	1414	2.456989	CATGAAGAATGGTTGCGCATC	58.543	47.619	12.75	11.18	32.10	3.91
1610	1703	6.870971	TCACCTAGTTTAAATGTTGGTCAC	57.129	37.500	0.00	0.00	0.00	3.67
1705	1810	7.651808	TGAGGAATTCAGAAACTTTTGATCAC	58.348	34.615	7.93	0.00	0.00	3.06
1789	1894	4.208632	GCGTAGAGCCAAGTGCAT	57.791	55.556	0.00	0.00	44.83	3.96
1913	2019	5.596836	ATGCTGAAACTTTTTGTGGAAGA	57.403	34.783	0.00	0.00	0.00	2.87
2055	2161	2.557924	TGTCATGGAAAATGTGCCTCAC	59.442	45.455	0.00	0.00	34.56	3.51
2060	2166	2.642311	TGGAAAATGTGCCTCACCTCTA	59.358	45.455	0.00	0.00	32.73	2.43
2092	2198	7.379750	GTTTACACCTGGTGCCAAAATAAATA	58.620	34.615	26.20	4.66	36.98	1.40
2223	2332	2.661718	CAGGTTTGTGGTGTTTAGGGT	58.338	47.619	0.00	0.00	0.00	4.34
2231	2340	0.887387	GGTGTTTAGGGTTGCGCTGA	60.887	55.000	9.73	0.00	0.00	4.26
2244	2353	1.480545	TGCGCTGATAACTGCTAGGAA	59.519	47.619	9.73	0.00	38.52	3.36
2345	2458	0.383949	ACCGTGAATGTTTGCACACC	59.616	50.000	0.00	0.00	35.03	4.16
2388	2501	5.728471	TGTTTTGCACTGAAATTTTGGAGA	58.272	33.333	0.00	0.00	0.00	3.71

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
41	42	9.653516	AATGTTGGATTTGGTGGAATATACATA	57.346	29.630	0.00	0.00	0.00	2.29
48	49	4.202440	TGCAAATGTTGGATTTGGTGGAAT	60.202	37.500	8.74	0.00	38.91	3.01
72	73	6.364976	GGAGTATTGTGTTATTTGTTGTTGCC	59.635	38.462	0.00	0.00	0.00	4.52
123	124	2.366916	CTGGAGTAGCTGATAACCCCTG	59.633	54.545	0.00	0.00	0.00	4.45
135	136	3.045601	ACATGACAACACTGGAGTAGC	57.954	47.619	0.00	0.00	0.00	3.58
149	150	6.402658	GCCTAGTAAGAAGCAAGAAACATGAC	60.403	42.308	0.00	0.00	0.00	3.06
164	165	0.616679	AACGCCCAGGCCTAGTAAGA	60.617	55.000	3.98	0.00	37.98	2.10
189	190	5.815222	ACAAAATAACCAAACAGCAGAAACC	59.185	36.000	0.00	0.00	0.00	3.27
196	197	7.971722	ACCGAATATACAAAATAACCAAACAGC	59.028	33.333	0.00	0.00	0.00	4.40
202	203	8.734218	TGCTAACCGAATATACAAAATAACCA	57.266	30.769	0.00	0.00	0.00	3.67
252	253	6.022217	CGAAGTTTCGGCTAGTAGATTTTC	57.978	41.667	0.00	0.00	46.30	2.29
282	283	4.113354	CCGAAAACCAAACCGAATTTTCA	58.887	39.130	8.52	0.00	39.80	2.69
288	289	3.693578	AGTAAACCGAAAACCAAACCGAA	59.306	39.130	0.00	0.00	0.00	4.30
374	375	7.109501	TCCCATCGATTTCTTGTCTAAAATCA	58.890	34.615	0.00	0.00	40.36	2.57
384	385	5.048782	TGTTTCTGTTCCCATCGATTTCTTG	60.049	40.000	0.00	0.00	0.00	3.02
393	394	6.659242	TCCTATTCTTTGTTTCTGTTCCCATC	59.341	38.462	0.00	0.00	0.00	3.51
401	402	8.020819	TGCGTTTATTCCTATTCTTTGTTTCTG	58.979	33.333	0.00	0.00	0.00	3.02
411	412	4.875544	TGTGCTGCGTTTATTCCTATTC	57.124	40.909	0.00	0.00	0.00	1.75
417	418	2.420022	ACCAGATGTGCTGCGTTTATTC	59.580	45.455	0.00	0.00	43.50	1.75
424	425	3.129502	CCCACCAGATGTGCTGCG	61.130	66.667	0.00	0.00	44.01	5.18
441	442	1.160137	AAACTTCACAGATGAGCGCC	58.840	50.000	2.29	0.00	35.83	6.53
449	450	3.192422	CCACCACAACAAAACTTCACAGA	59.808	43.478	0.00	0.00	0.00	3.41
451	452	2.894126	ACCACCACAACAAAACTTCACA	59.106	40.909	0.00	0.00	0.00	3.58
454	455	2.494073	TCCACCACCACAACAAAACTTC	59.506	45.455	0.00	0.00	0.00	3.01
460	461	0.395036	CCACTCCACCACCACAACAA	60.395	55.000	0.00	0.00	0.00	2.83
465	466	1.005394	CGTACCACTCCACCACCAC	60.005	63.158	0.00	0.00	0.00	4.16
466	467	2.874664	GCGTACCACTCCACCACCA	61.875	63.158	0.00	0.00	0.00	4.17
467	468	2.047560	GCGTACCACTCCACCACC	60.048	66.667	0.00	0.00	0.00	4.61
562	569	0.811616	CCACTCGTGCTAATCTGCCC	60.812	60.000	0.00	0.00	0.00	5.36
565	572	1.148157	CCGCCACTCGTGCTAATCTG	61.148	60.000	0.00	0.00	36.19	2.90
589	596	2.027751	GATGGGCTCGACTACGCC	59.972	66.667	4.87	4.87	45.55	5.68
590	597	0.249489	ATTGATGGGCTCGACTACGC	60.249	55.000	0.00	0.00	39.58	4.42
591	598	2.128035	GAATTGATGGGCTCGACTACG	58.872	52.381	0.00	0.00	41.26	3.51
592	599	3.179443	TGAATTGATGGGCTCGACTAC	57.821	47.619	0.00	0.00	0.00	2.73
593	600	3.904800	TTGAATTGATGGGCTCGACTA	57.095	42.857	0.00	0.00	0.00	2.59
594	601	2.787473	TTGAATTGATGGGCTCGACT	57.213	45.000	0.00	0.00	0.00	4.18
595	602	4.107622	CAATTTGAATTGATGGGCTCGAC	58.892	43.478	10.22	0.00	46.72	4.20
596	603	3.130869	CCAATTTGAATTGATGGGCTCGA	59.869	43.478	16.00	0.00	46.72	4.04
597	604	3.450578	CCAATTTGAATTGATGGGCTCG	58.549	45.455	16.00	0.00	46.72	5.03
598	605	3.198417	ACCCAATTTGAATTGATGGGCTC	59.802	43.478	16.00	0.00	46.72	4.70
599	606	3.183801	ACCCAATTTGAATTGATGGGCT	58.816	40.909	16.00	1.37	46.72	5.19
600	607	3.632643	ACCCAATTTGAATTGATGGGC	57.367	42.857	16.00	0.00	46.72	5.36
601	608	9.850198	ATAATTAACCCAATTTGAATTGATGGG	57.150	29.630	16.00	12.54	46.72	4.00
609	616	9.225436	GCAAAAGGATAATTAACCCAATTTGAA	57.775	29.630	24.19	0.00	37.93	2.69
610	617	7.826744	GGCAAAAGGATAATTAACCCAATTTGA	59.173	33.333	24.19	0.00	37.93	2.69
611	618	7.066887	GGGCAAAAGGATAATTAACCCAATTTG	59.933	37.037	19.85	19.85	37.93	2.32
612	619	7.036935	AGGGCAAAAGGATAATTAACCCAATTT	60.037	33.333	8.09	5.38	37.93	1.82
613	620	6.446759	AGGGCAAAAGGATAATTAACCCAATT	59.553	34.615	8.09	0.00	40.10	2.32
614	621	5.970021	AGGGCAAAAGGATAATTAACCCAAT	59.030	36.000	8.09	0.00	37.28	3.16
686	693	1.276989	CACGGACTAGGGGCAAAACTA	59.723	52.381	0.00	0.00	0.00	2.24
782	792	2.753009	AATTGGCCGTCTCTGCTGCA	62.753	55.000	0.88	0.88	0.00	4.41
785	795	2.489938	TAAAATTGGCCGTCTCTGCT	57.510	45.000	0.00	0.00	0.00	4.24
1054	1140	1.070758	ACAGACGAAGACAGGCATGTT	59.929	47.619	5.07	0.00	40.68	2.71
1196	1282	1.642762	ACCCATTGCTCAAAGATCCCT	59.357	47.619	0.00	0.00	0.00	4.20
1359	1449	3.632333	TCGCCCTTCATCTCTTCTTCTA	58.368	45.455	0.00	0.00	0.00	2.10
1789	1894	2.092968	CAGTTGGCCCATTAGTCTAGCA	60.093	50.000	0.00	0.00	0.00	3.49
1913	2019	8.980596	TGTTTGGCTCTGGAATAATTCAATTAT	58.019	29.630	0.00	0.00	37.05	1.28
2060	2166	2.302157	GCACCAGGTGTAAACCTCTACT	59.698	50.000	21.26	0.00	38.22	2.57
2204	2313	3.028130	CAACCCTAAACACCACAAACCT	58.972	45.455	0.00	0.00	0.00	3.50
2223	2332	1.480545	TCCTAGCAGTTATCAGCGCAA	59.519	47.619	11.47	0.00	35.48	4.85
2231	2340	4.778213	TGCCATCTTTCCTAGCAGTTAT	57.222	40.909	0.00	0.00	0.00	1.89
2244	2353	3.508793	CCATGTCAAAGTCTTGCCATCTT	59.491	43.478	0.00	0.00	28.75	2.40
2316	2429	5.334879	GCAAACATTCACGGTCTCACTATTT	60.335	40.000	0.00	0.00	0.00	1.40
2317	2430	4.154195	GCAAACATTCACGGTCTCACTATT	59.846	41.667	0.00	0.00	0.00	1.73
2318	2431	3.684788	GCAAACATTCACGGTCTCACTAT	59.315	43.478	0.00	0.00	0.00	2.12
2345	2458	2.256117	AAGGAAAACCACTCTCACGG	57.744	50.000	0.00	0.00	0.00	4.94
2388	2501	4.885325	ACATACGTTTTCAACCTTCCAACT	59.115	37.500	0.00	0.00	0.00	3.16

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.