AutoCloner

Multiple sequence alignment - TraesCS7A01G484400

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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	TraesCS7A01G484400	chr7A	100.000	2943	0	0	1	2943	675493266	675496208	0.000000e+00	5435
1	TraesCS7A01G484400	chr7A	85.247	2447	300	47	532	2943	102054804	102057224	0.000000e+00	2462
2	TraesCS7A01G484400	chr7D	95.338	2960	90	21	1	2943	86074160	86071232	0.000000e+00	4658
3	TraesCS7A01G484400	chr2D	94.150	2342	79	26	1	2311	431393373	431391059	0.000000e+00	3513
4	TraesCS7A01G484400	chr2B	88.881	1331	136	7	676	1999	259685259	259686584	0.000000e+00	1628
5	TraesCS7A01G484400	chr2B	88.457	849	84	9	2104	2942	259686965	259687809	0.000000e+00	1013
6	TraesCS7A01G484400	chr2B	81.951	687	87	21	1	674	259679495	259680157	5.550000e-152	547
7	TraesCS7A01G484400	chr2B	75.940	266	52	11	2660	2921	11907851	11908108	3.080000e-25	126
8	TraesCS7A01G484400	chrUn	85.218	1468	179	26	541	1988	48373267	48371818	0.000000e+00	1474
9	TraesCS7A01G484400	chrUn	85.450	1244	152	21	761	1988	318400545	318401775	0.000000e+00	1267
10	TraesCS7A01G484400	chrUn	95.531	179	7	1	1	178	24274137	24274315	4.800000e-73	285
11	TraesCS7A01G484400	chr5B	88.647	1101	105	15	1857	2942	126444430	126445525	0.000000e+00	1323
12	TraesCS7A01G484400	chr5B	84.488	1212	138	23	2	1188	126443243	126444429	0.000000e+00	1151
13	TraesCS7A01G484400	chr1A	86.572	849	95	14	1146	1987	570105510	570104674	0.000000e+00	918
14	TraesCS7A01G484400	chr5A	81.635	795	145	1	1003	1797	570228446	570227653	0.000000e+00	658
15	TraesCS7A01G484400	chr5A	82.799	593	84	11	532	1112	541366201	541366787	5.620000e-142	514
16	TraesCS7A01G484400	chr3B	77.819	1073	209	20	1003	2065	232563370	232564423	1.150000e-178	636

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	TraesCS7A01G484400	chr7A	675493266	675496208	2942	False	5435.0	5435	100.0000	1	2943	1	chr7A.!!$F2	2942
1	TraesCS7A01G484400	chr7A	102054804	102057224	2420	False	2462.0	2462	85.2470	532	2943	1	chr7A.!!$F1	2411
2	TraesCS7A01G484400	chr7D	86071232	86074160	2928	True	4658.0	4658	95.3380	1	2943	1	chr7D.!!$R1	2942
3	TraesCS7A01G484400	chr2D	431391059	431393373	2314	True	3513.0	3513	94.1500	1	2311	1	chr2D.!!$R1	2310
4	TraesCS7A01G484400	chr2B	259685259	259687809	2550	False	1320.5	1628	88.6690	676	2942	2	chr2B.!!$F3	2266
5	TraesCS7A01G484400	chr2B	259679495	259680157	662	False	547.0	547	81.9510	1	674	1	chr2B.!!$F2	673
6	TraesCS7A01G484400	chrUn	48371818	48373267	1449	True	1474.0	1474	85.2180	541	1988	1	chrUn.!!$R1	1447
7	TraesCS7A01G484400	chrUn	318400545	318401775	1230	False	1267.0	1267	85.4500	761	1988	1	chrUn.!!$F2	1227
8	TraesCS7A01G484400	chr5B	126443243	126445525	2282	False	1237.0	1323	86.5675	2	2942	2	chr5B.!!$F1	2940
9	TraesCS7A01G484400	chr1A	570104674	570105510	836	True	918.0	918	86.5720	1146	1987	1	chr1A.!!$R1	841
10	TraesCS7A01G484400	chr5A	570227653	570228446	793	True	658.0	658	81.6350	1003	1797	1	chr5A.!!$R1	794
11	TraesCS7A01G484400	chr5A	541366201	541366787	586	False	514.0	514	82.7990	532	1112	1	chr5A.!!$F1	580
12	TraesCS7A01G484400	chr3B	232563370	232564423	1053	False	636.0	636	77.8190	1003	2065	1	chr3B.!!$F1	1062

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
480	502	0.034337	GTAGTTCAGGTTCGCCCACA	59.966	55.0	0.0	0.0	38.27	4.17	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1954	2010	0.458669	CCTATCCGCGGTGTTACACT	59.541	55.0	27.15	3.46	34.4	3.55	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
117	119	4.228567	GCCCTAGCCCTCTGACGC	62.229	72.222	0.00	0.00	0.00	5.19
121	123	0.460987	CCTAGCCCTCTGACGCAAAG	60.461	60.000	0.00	0.00	0.00	2.77
144	146	0.748005	GGCATGTACTTGATGGGCGT	60.748	55.000	12.65	0.00	0.00	5.68
185	187	1.746615	GCCGTGGAGACATGCATGT	60.747	57.895	31.82	31.82	46.34	3.21
226	240	2.320681	TGGACTACCACAGGCTTAGT	57.679	50.000	0.00	0.00	41.77	2.24
229	243	4.359105	TGGACTACCACAGGCTTAGTAAT	58.641	43.478	0.00	0.00	41.77	1.89
389	410	4.457257	TCATGGCACGACATTTTTCATGTA	59.543	37.500	0.00	0.00	34.11	2.29
450	472	6.097839	AGGCTTGTCGTAGTCAGGATTAATTA	59.902	38.462	0.00	0.00	0.00	1.40
451	473	6.421202	GGCTTGTCGTAGTCAGGATTAATTAG	59.579	42.308	0.00	0.00	0.00	1.73
452	474	6.074249	GCTTGTCGTAGTCAGGATTAATTAGC	60.074	42.308	0.00	0.00	0.00	3.09
453	475	5.516996	TGTCGTAGTCAGGATTAATTAGCG	58.483	41.667	0.00	0.00	0.00	4.26
454	476	5.297527	TGTCGTAGTCAGGATTAATTAGCGA	59.702	40.000	0.00	0.00	0.00	4.93
455	477	5.852229	GTCGTAGTCAGGATTAATTAGCGAG	59.148	44.000	0.00	0.00	0.00	5.03
456	478	5.761726	TCGTAGTCAGGATTAATTAGCGAGA	59.238	40.000	0.00	0.00	0.00	4.04
457	479	5.852229	CGTAGTCAGGATTAATTAGCGAGAC	59.148	44.000	0.00	0.00	0.00	3.36
458	480	5.854010	AGTCAGGATTAATTAGCGAGACA	57.146	39.130	0.00	0.00	0.00	3.41
459	481	6.412362	AGTCAGGATTAATTAGCGAGACAT	57.588	37.500	0.00	0.00	0.00	3.06
460	482	6.451393	AGTCAGGATTAATTAGCGAGACATC	58.549	40.000	0.00	0.00	0.00	3.06
472	494	3.489180	CGAGACATCGTAGTTCAGGTT	57.511	47.619	0.00	0.00	44.09	3.50
473	495	3.427243	CGAGACATCGTAGTTCAGGTTC	58.573	50.000	0.00	0.00	44.09	3.62
474	496	3.427243	GAGACATCGTAGTTCAGGTTCG	58.573	50.000	0.00	0.00	0.00	3.95
475	497	1.918609	GACATCGTAGTTCAGGTTCGC	59.081	52.381	0.00	0.00	0.00	4.70
476	498	1.278238	CATCGTAGTTCAGGTTCGCC	58.722	55.000	0.00	0.00	37.60	5.54
477	499	0.175073	ATCGTAGTTCAGGTTCGCCC	59.825	55.000	0.00	0.00	38.27	6.13
478	500	1.180456	TCGTAGTTCAGGTTCGCCCA	61.180	55.000	0.00	0.00	38.27	5.36
479	501	1.012486	CGTAGTTCAGGTTCGCCCAC	61.012	60.000	0.00	0.00	38.27	4.61
480	502	0.034337	GTAGTTCAGGTTCGCCCACA	59.966	55.000	0.00	0.00	38.27	4.17
481	503	0.981183	TAGTTCAGGTTCGCCCACAT	59.019	50.000	0.00	0.00	38.27	3.21
482	504	0.110486	AGTTCAGGTTCGCCCACATT	59.890	50.000	0.00	0.00	38.27	2.71
483	505	1.349688	AGTTCAGGTTCGCCCACATTA	59.650	47.619	0.00	0.00	38.27	1.90
484	506	1.737793	GTTCAGGTTCGCCCACATTAG	59.262	52.381	0.00	0.00	38.27	1.73
485	507	0.981183	TCAGGTTCGCCCACATTAGT	59.019	50.000	0.00	0.00	38.27	2.24
486	508	1.066430	TCAGGTTCGCCCACATTAGTC	60.066	52.381	0.00	0.00	38.27	2.59
487	509	0.981183	AGGTTCGCCCACATTAGTCA	59.019	50.000	0.00	0.00	38.27	3.41
488	510	1.066143	AGGTTCGCCCACATTAGTCAG	60.066	52.381	0.00	0.00	38.27	3.51
489	511	1.369625	GTTCGCCCACATTAGTCAGG	58.630	55.000	0.00	0.00	0.00	3.86
490	512	1.066430	GTTCGCCCACATTAGTCAGGA	60.066	52.381	0.00	0.00	0.00	3.86
491	513	1.496060	TCGCCCACATTAGTCAGGAT	58.504	50.000	0.00	0.00	0.00	3.24
492	514	1.837439	TCGCCCACATTAGTCAGGATT	59.163	47.619	0.00	0.00	0.00	3.01
493	515	2.238646	TCGCCCACATTAGTCAGGATTT	59.761	45.455	0.00	0.00	0.00	2.17
674	708	1.997606	GTCACGCAATTTACTACGCCT	59.002	47.619	0.00	0.00	0.00	5.52
689	726	1.767692	GCCTTTTCACCCCTCCTCA	59.232	57.895	0.00	0.00	0.00	3.86
801	839	2.110213	AAAGGCGGACGAACAGCA	59.890	55.556	0.00	0.00	41.24	4.41
865	903	4.767255	GTCAGTCAGCCGGGGCAG	62.767	72.222	12.97	3.82	44.88	4.85
961	1006	7.340487	TCACTGTTCTTAGATCTTGCTCTCATA	59.660	37.037	0.00	0.00	0.00	2.15
962	1007	7.434897	CACTGTTCTTAGATCTTGCTCTCATAC	59.565	40.741	0.00	0.00	0.00	2.39
998	1044	3.105283	TCAAGGGGCCTTAGTTCTAGAC	58.895	50.000	0.84	0.00	34.50	2.59
1000	1046	1.287146	AGGGGCCTTAGTTCTAGACGA	59.713	52.381	0.84	0.00	0.00	4.20
1395	1444	1.347378	GTTTTTGGCATCCCATGTGGT	59.653	47.619	0.00	0.00	41.78	4.16
1536	1585	2.145958	ATCGAGCCATCACAGAATCG	57.854	50.000	0.00	0.00	0.00	3.34
1729	1778	1.202806	TGTTCCAAGCTGTGAGGAAGG	60.203	52.381	9.63	0.00	41.74	3.46
1813	1862	6.072112	TGCAGGTATTTTTCACTCTGTTTC	57.928	37.500	0.00	0.00	0.00	2.78
1814	1863	5.592282	TGCAGGTATTTTTCACTCTGTTTCA	59.408	36.000	0.00	0.00	0.00	2.69
1815	1864	6.145535	GCAGGTATTTTTCACTCTGTTTCAG	58.854	40.000	0.00	0.00	0.00	3.02
1816	1865	6.672147	CAGGTATTTTTCACTCTGTTTCAGG	58.328	40.000	0.00	0.00	31.51	3.86
1910	1966	8.032451	GCTAATGGGCTTTTTATCACAACTTTA	58.968	33.333	0.00	0.00	0.00	1.85
1954	2010	2.350007	GGCGTTCTAAACATGTTGCGAA	60.350	45.455	12.82	14.25	0.00	4.70
2260	2602	2.560119	GGGAAACGCCACATGCACA	61.560	57.895	0.00	0.00	41.33	4.57
2640	2983	7.804843	TGGAAAACGAAGGAACAAATACTTA	57.195	32.000	0.00	0.00	0.00	2.24
2645	2988	6.882458	ACGAAGGAACAAATACTTACGATC	57.118	37.500	0.00	0.00	0.00	3.69
2681	3024	8.853077	TGTATCAACAGATCAAACTCAATTCT	57.147	30.769	0.00	0.00	0.00	2.40
2792	3136	8.786937	AAATTTGAATGCATATACACGATGAC	57.213	30.769	0.00	0.00	0.00	3.06

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
117	119	2.161855	TCAAGTACATGCCAGCCTTTG	58.838	47.619	0.00	0.00	0.00	2.77
121	123	1.027357	CCATCAAGTACATGCCAGCC	58.973	55.000	0.00	0.00	0.00	4.85
144	146	2.567985	GAACAAGTTCCAAACGGAGGA	58.432	47.619	1.51	0.00	32.88	3.71
185	187	2.251963	CAACGCTTGCATGCACGA	59.748	55.556	30.25	14.02	0.00	4.35
226	240	2.028476	CAGTGGTCCACGTCCTCAATTA	60.028	50.000	16.44	0.00	39.64	1.40
229	243	1.745890	CAGTGGTCCACGTCCTCAA	59.254	57.895	16.44	0.00	39.64	3.02
284	299	2.705658	ACAACCTCATTGACCTGTGAGA	59.294	45.455	4.08	0.00	43.50	3.27
342	357	6.656632	TGGCAGGTAATTTTTGTGAATACA	57.343	33.333	0.00	0.00	34.31	2.29
389	410	8.822805	TGTTCCACTTTATCTAACTTGATAGGT	58.177	33.333	0.00	0.00	31.51	3.08
453	475	3.427243	CGAACCTGAACTACGATGTCTC	58.573	50.000	0.00	0.00	0.00	3.36
454	476	2.415625	GCGAACCTGAACTACGATGTCT	60.416	50.000	0.00	0.00	0.00	3.41
455	477	1.918609	GCGAACCTGAACTACGATGTC	59.081	52.381	0.00	0.00	0.00	3.06
456	478	1.403780	GGCGAACCTGAACTACGATGT	60.404	52.381	0.00	0.00	0.00	3.06
457	479	1.278238	GGCGAACCTGAACTACGATG	58.722	55.000	0.00	0.00	0.00	3.84
458	480	0.175073	GGGCGAACCTGAACTACGAT	59.825	55.000	0.00	0.00	35.85	3.73
459	481	1.180456	TGGGCGAACCTGAACTACGA	61.180	55.000	0.00	0.00	41.11	3.43
460	482	1.012486	GTGGGCGAACCTGAACTACG	61.012	60.000	0.00	0.00	41.11	3.51
461	483	0.034337	TGTGGGCGAACCTGAACTAC	59.966	55.000	0.00	0.00	41.11	2.73
462	484	0.981183	ATGTGGGCGAACCTGAACTA	59.019	50.000	0.00	0.00	41.11	2.24
464	486	1.737793	CTAATGTGGGCGAACCTGAAC	59.262	52.381	0.00	0.00	41.11	3.18
467	489	1.338674	TGACTAATGTGGGCGAACCTG	60.339	52.381	0.00	0.00	41.11	4.00
468	490	0.981183	TGACTAATGTGGGCGAACCT	59.019	50.000	0.00	0.00	41.11	3.50
469	491	1.369625	CTGACTAATGTGGGCGAACC	58.630	55.000	0.00	0.00	40.81	3.62
470	492	1.066430	TCCTGACTAATGTGGGCGAAC	60.066	52.381	0.00	0.00	0.00	3.95
471	493	1.271856	TCCTGACTAATGTGGGCGAA	58.728	50.000	0.00	0.00	0.00	4.70
472	494	1.496060	ATCCTGACTAATGTGGGCGA	58.504	50.000	0.00	0.00	0.00	5.54
473	495	2.332063	AATCCTGACTAATGTGGGCG	57.668	50.000	0.00	0.00	0.00	6.13
474	496	5.376625	TGATAAATCCTGACTAATGTGGGC	58.623	41.667	0.00	0.00	0.00	5.36
475	497	6.484643	CACTGATAAATCCTGACTAATGTGGG	59.515	42.308	0.00	0.00	0.00	4.61
476	498	7.050377	ACACTGATAAATCCTGACTAATGTGG	58.950	38.462	0.00	0.00	0.00	4.17
477	499	8.498054	AACACTGATAAATCCTGACTAATGTG	57.502	34.615	0.00	0.00	0.00	3.21
478	500	9.520515	AAAACACTGATAAATCCTGACTAATGT	57.479	29.630	0.00	0.00	0.00	2.71
674	708	1.420138	GACAGTGAGGAGGGGTGAAAA	59.580	52.381	0.00	0.00	0.00	2.29
689	726	1.043673	GGGGCGAGGTAGATGACAGT	61.044	60.000	0.00	0.00	0.00	3.55
831	869	0.106318	GACGGAGGAGGGTAAGCCTA	60.106	60.000	0.00	0.00	33.84	3.93
863	901	1.834263	AGTACCTCTTGCTTAGGCCTG	59.166	52.381	17.99	0.00	37.67	4.85
865	903	1.831736	TGAGTACCTCTTGCTTAGGCC	59.168	52.381	0.00	0.00	37.67	5.19
866	904	2.418884	GGTGAGTACCTCTTGCTTAGGC	60.419	54.545	0.00	0.00	43.97	3.93
867	905	3.528597	GGTGAGTACCTCTTGCTTAGG	57.471	52.381	0.00	0.00	43.97	2.69
961	1006	6.012421	GGCCCCTTGATTAGAAATCCTATAGT	60.012	42.308	0.00	0.00	0.00	2.12
962	1007	6.216456	AGGCCCCTTGATTAGAAATCCTATAG	59.784	42.308	0.00	0.00	0.00	1.31
976	1021	3.712218	GTCTAGAACTAAGGCCCCTTGAT	59.288	47.826	9.79	0.00	37.47	2.57
998	1044	8.217115	CACTAAATAAATCGGACATCTTCATCG	58.783	37.037	0.00	0.00	0.00	3.84
1000	1046	7.445402	CCCACTAAATAAATCGGACATCTTCAT	59.555	37.037	0.00	0.00	0.00	2.57
1395	1444	6.382859	TGCCTTCACCTTCTATGACTGTATTA	59.617	38.462	0.00	0.00	0.00	0.98
1536	1585	4.020543	AGTCCTTCTCTATCTGTGTGGAC	58.979	47.826	0.00	0.00	41.95	4.02
1729	1778	3.141398	TCTTGGACACATCTGCTTTGAC	58.859	45.455	0.00	0.00	0.00	3.18
1838	1890	7.372451	TCTGAATAACATCAAAAAGTACGGG	57.628	36.000	0.00	0.00	0.00	5.28
1910	1966	7.307870	CGCCTAGATCAAGACTATTTAGTACGT	60.308	40.741	0.00	0.00	36.50	3.57
1918	1974	7.584122	TTAGAACGCCTAGATCAAGACTATT	57.416	36.000	0.00	0.00	0.00	1.73
1954	2010	0.458669	CCTATCCGCGGTGTTACACT	59.541	55.000	27.15	3.46	34.40	3.55
2102	2434	9.825109	ATGTCATGAATGAAAATGATTGCATTA	57.175	25.926	0.00	0.00	43.52	1.90
2260	2602	2.450609	AACTACTTCGCAACATCGGT	57.549	45.000	0.00	0.00	0.00	4.69
2393	2736	3.254903	GGTTAGTTGCGAGGGAAAACAAT	59.745	43.478	0.00	0.00	0.00	2.71
2623	2966	5.233689	GGGATCGTAAGTATTTGTTCCTTCG	59.766	44.000	0.00	0.00	39.48	3.79
2753	3096	8.695284	TGCATTCAAATTTCATAACGTAAACAC	58.305	29.630	0.00	0.00	0.00	3.32
2792	3136	3.652057	AATGGGTAGTGTCAGATTGGG	57.348	47.619	0.00	0.00	0.00	4.12
2864	3208	4.529897	TGCTTGATGATAAACTGCCATCT	58.470	39.130	0.00	0.00	37.97	2.90

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.