AutoCloner

Multiple sequence alignment - TraesCS2A01G249900

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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	TraesCS2A01G249900	chr2A	100.000	3396	0	0	1	3396	376111399	376108004	0.000000e+00	6272.0
1	TraesCS2A01G249900	chr2A	88.000	225	19	8	2628	2847	242428562	242428341	3.360000e-65	259.0
2	TraesCS2A01G249900	chr2A	87.946	224	21	6	2628	2847	591275614	591275393	3.360000e-65	259.0
3	TraesCS2A01G249900	chr2A	78.829	222	20	11	2627	2847	4218496	4218301	1.280000e-24	124.0
4	TraesCS2A01G249900	chr2A	95.238	42	2	0	2449	2490	315809796	315809755	2.190000e-07	67.6
5	TraesCS2A01G249900	chr2D	95.974	2484	59	10	946	3396	299898273	299895798	0.000000e+00	3995.0
6	TraesCS2A01G249900	chr2D	90.252	913	76	8	1	901	563966710	563965799	0.000000e+00	1181.0
7	TraesCS2A01G249900	chr2D	90.033	913	80	8	1	903	525938952	525939863	0.000000e+00	1171.0
8	TraesCS2A01G249900	chr2D	95.349	43	2	0	2449	2491	360992128	360992170	6.080000e-08	69.4
9	TraesCS2A01G249900	chr2B	96.757	1141	20	3	902	2027	371155318	371156456	0.000000e+00	1886.0
10	TraesCS2A01G249900	chr2B	94.654	767	22	2	2648	3396	371158629	371159394	0.000000e+00	1171.0
11	TraesCS2A01G249900	chr2B	95.426	634	16	3	2009	2635	371158016	371158643	0.000000e+00	998.0
12	TraesCS2A01G249900	chr2B	100.000	33	0	0	2849	2881	794383445	794383413	1.020000e-05	62.1
13	TraesCS2A01G249900	chr4D	91.280	906	74	4	1	901	477227191	477226286	0.000000e+00	1230.0
14	TraesCS2A01G249900	chr4D	90.789	912	75	7	1	904	81327877	81326967	0.000000e+00	1210.0
15	TraesCS2A01G249900	chr7D	91.109	911	72	7	1	903	182600328	182599419	0.000000e+00	1225.0
16	TraesCS2A01G249900	chr7D	90.611	916	73	8	1	904	630613394	630612480	0.000000e+00	1203.0
17	TraesCS2A01G249900	chr7D	90.231	911	71	9	1	901	69047128	69048030	0.000000e+00	1173.0
18	TraesCS2A01G249900	chr6A	90.739	907	74	7	1	899	162791031	162790127	0.000000e+00	1201.0
19	TraesCS2A01G249900	chr6D	90.121	911	76	9	1	904	10675393	10674490	0.000000e+00	1171.0
20	TraesCS2A01G249900	chr5A	88.444	225	18	8	2628	2847	210535659	210535438	7.230000e-67	265.0
21	TraesCS2A01G249900	chr5A	93.333	45	3	0	2449	2493	78965502	78965458	2.190000e-07	67.6
22	TraesCS2A01G249900	chr3A	88.393	224	20	6	2628	2847	114570764	114570985	7.230000e-67	265.0
23	TraesCS2A01G249900	chr3A	88.000	225	19	8	2628	2847	560917465	560917244	3.360000e-65	259.0
24	TraesCS2A01G249900	chr7B	88.000	225	19	8	2628	2847	559265021	559264800	3.360000e-65	259.0
25	TraesCS2A01G249900	chr5D	88.000	225	19	8	2628	2847	201312240	201312019	3.360000e-65	259.0
26	TraesCS2A01G249900	chr1B	97.674	43	1	0	2449	2491	547029500	547029458	1.310000e-09	75.0
27	TraesCS2A01G249900	chr5B	95.349	43	2	0	2449	2491	81370511	81370553	6.080000e-08	69.4
28	TraesCS2A01G249900	chr4B	95.349	43	2	0	2449	2491	483511767	483511809	6.080000e-08	69.4
29	TraesCS2A01G249900	chr1D	93.023	43	3	0	2449	2491	274943969	274943927	2.830000e-06	63.9
30	TraesCS2A01G249900	chr7A	100.000	31	0	0	2851	2881	99646344	99646314	1.320000e-04	58.4
31	TraesCS2A01G249900	chr4A	100.000	30	0	0	2849	2878	16294732	16294761	4.730000e-04	56.5

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	TraesCS2A01G249900	chr2A	376108004	376111399	3395	True	6272.000000	6272	100.000000	1	3396	1	chr2A.!!$R4	3395
1	TraesCS2A01G249900	chr2D	299895798	299898273	2475	True	3995.000000	3995	95.974000	946	3396	1	chr2D.!!$R1	2450
2	TraesCS2A01G249900	chr2D	563965799	563966710	911	True	1181.000000	1181	90.252000	1	901	1	chr2D.!!$R2	900
3	TraesCS2A01G249900	chr2D	525938952	525939863	911	False	1171.000000	1171	90.033000	1	903	1	chr2D.!!$F2	902
4	TraesCS2A01G249900	chr2B	371155318	371159394	4076	False	1351.666667	1886	95.612333	902	3396	3	chr2B.!!$F1	2494
5	TraesCS2A01G249900	chr4D	477226286	477227191	905	True	1230.000000	1230	91.280000	1	901	1	chr4D.!!$R2	900
6	TraesCS2A01G249900	chr4D	81326967	81327877	910	True	1210.000000	1210	90.789000	1	904	1	chr4D.!!$R1	903
7	TraesCS2A01G249900	chr7D	182599419	182600328	909	True	1225.000000	1225	91.109000	1	903	1	chr7D.!!$R1	902
8	TraesCS2A01G249900	chr7D	630612480	630613394	914	True	1203.000000	1203	90.611000	1	904	1	chr7D.!!$R2	903
9	TraesCS2A01G249900	chr7D	69047128	69048030	902	False	1173.000000	1173	90.231000	1	901	1	chr7D.!!$F1	900
10	TraesCS2A01G249900	chr6A	162790127	162791031	904	True	1201.000000	1201	90.739000	1	899	1	chr6A.!!$R1	898
11	TraesCS2A01G249900	chr6D	10674490	10675393	903	True	1171.000000	1171	90.121000	1	904	1	chr6D.!!$R1	903

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
844	867	0.318275	GCGCCAAACCAAACGATGAA	60.318	50.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2551	4178	1.153745	GCAGTAGCGAGGGAGTGTG	60.154	63.158	0.0	0.0	0.0	3.82	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
103	104	3.492482	GGTGCAGTTTGTAGCAAATGGTT	60.492	43.478	0.00	0.00	43.20	3.67
110	111	6.922957	CAGTTTGTAGCAAATGGTTGTACATT	59.077	34.615	0.00	0.00	42.56	2.71
120	121	7.601856	CAAATGGTTGTACATTCAACTATGGT	58.398	34.615	0.00	0.10	44.48	3.55
223	224	1.603456	TTTCCACAATGCTCAAGCGA	58.397	45.000	0.00	0.00	45.83	4.93
291	292	5.945784	CCAATTTTCTATTGTGAGAGGACCA	59.054	40.000	0.00	0.00	0.00	4.02
335	336	1.468520	GCTTTGGTACATCATGCACGT	59.531	47.619	0.00	0.00	39.30	4.49
430	431	2.214181	GAGACATCCCGTGCGAGTGT	62.214	60.000	0.00	0.00	0.00	3.55
484	485	2.355513	GCCTCCTATCATGCCATTCGAT	60.356	50.000	0.00	0.00	0.00	3.59
487	488	4.081476	CCTCCTATCATGCCATTCGATGTA	60.081	45.833	0.00	0.00	0.00	2.29
495	496	0.809636	CCATTCGATGTACCGCAGCA	60.810	55.000	0.00	0.00	32.00	4.41
506	507	0.816825	ACCGCAGCACATGATGATCC	60.817	55.000	0.00	0.00	32.25	3.36
508	509	1.306148	CGCAGCACATGATGATCCTT	58.694	50.000	0.00	0.00	32.25	3.36
514	515	5.608449	CAGCACATGATGATCCTTAGAAGA	58.392	41.667	0.00	0.00	32.25	2.87
644	646	9.171701	TGTTGTATTAAACGATAAACTGTTTGC	57.828	29.630	15.69	6.92	38.64	3.68
770	780	1.820233	GCTGCATTTTTGCGCGTTGT	61.820	50.000	8.43	0.00	37.69	3.32
783	795	3.649986	GTTGTTGGAGCTGCGCGT	61.650	61.111	8.43	0.00	0.00	6.01
844	867	0.318275	GCGCCAAACCAAACGATGAA	60.318	50.000	0.00	0.00	0.00	2.57
855	879	4.717917	CGATGAACGGCGACAAAC	57.282	55.556	16.62	10.75	38.46	2.93
870	894	4.145997	CGACAAACTAATTTTTAGCGCGT	58.854	39.130	8.43	0.00	0.00	6.01
1261	1300	1.899437	GCATCCTTCGGTCTCCACCA	61.899	60.000	0.00	0.00	44.02	4.17
1550	1589	2.280592	GGCGAAGGGTGTGTCGTT	60.281	61.111	0.00	0.00	39.46	3.85
1639	1678	0.462047	GGGCGTTTCGAGATGGTCAT	60.462	55.000	0.00	0.00	0.00	3.06
1946	1987	0.601046	GATGATCCGGCAGCGATTGA	60.601	55.000	0.00	0.00	0.00	2.57
2196	3815	0.250209	CCGAGCTCATCCTTGATGGG	60.250	60.000	15.40	2.02	42.90	4.00
2395	4021	9.287373	ACGGATAAATAAAACCTTCAACACTTA	57.713	29.630	0.00	0.00	0.00	2.24
2401	4027	5.479716	AAAACCTTCAACACTTACTGTCG	57.520	39.130	0.00	0.00	30.29	4.35
2551	4178	3.248029	CAGACGTGAACTGCCAGC	58.752	61.111	0.00	0.00	0.00	4.85
2562	4189	3.947132	CTGCCAGCACACTCCCTCG	62.947	68.421	0.00	0.00	0.00	4.63
2627	4254	3.077359	CAAACACTAAGGGCTCCTTCAG	58.923	50.000	9.46	8.52	43.57	3.02
2630	4257	3.185455	ACACTAAGGGCTCCTTCAGAAT	58.815	45.455	9.46	0.00	43.57	2.40
2631	4258	3.589288	ACACTAAGGGCTCCTTCAGAATT	59.411	43.478	9.46	0.00	43.57	2.17
2632	4259	4.043435	ACACTAAGGGCTCCTTCAGAATTT	59.957	41.667	9.46	0.00	43.57	1.82
2635	4262	4.879197	AAGGGCTCCTTCAGAATTTTTG	57.121	40.909	0.99	0.00	40.17	2.44
2764	4391	9.852091	GATTTCTAGCATTCAATCAAACTCTTT	57.148	29.630	0.00	0.00	0.00	2.52
2766	4393	7.149569	TCTAGCATTCAATCAAACTCTTTGG	57.850	36.000	0.00	0.00	40.98	3.28
2865	4501	5.336929	CCAATCACATTTTGAGAATCCTGCA	60.337	40.000	0.00	0.00	37.77	4.41
3068	4722	9.052759	TCTTTCTAATGTTTTCAGTCCAAGTAC	57.947	33.333	0.00	0.00	0.00	2.73
3173	4827	1.659335	GTTCTCGTTGACGTCCGCA	60.659	57.895	14.12	0.00	40.80	5.69
3247	4901	3.199880	ACCATCCATCTGATCCGAAAC	57.800	47.619	0.00	0.00	0.00	2.78
3312	4966	4.412796	TCTTTGAAGCGATCCAGATCAT	57.587	40.909	8.31	0.00	37.69	2.45

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
19	20	3.745799	ACCGGTTGACAACATTGATGTA	58.254	40.909	19.58	0.00	40.80	2.29
110	111	6.822442	TCCGCAAGATAATAACCATAGTTGA	58.178	36.000	0.00	0.00	43.02	3.18
120	121	7.981789	GGATAGATGTCATCCGCAAGATAATAA	59.018	37.037	9.29	0.00	43.02	1.40
160	161	2.535574	GCTTTTTCAACGGCTTCACAAG	59.464	45.455	0.00	0.00	0.00	3.16
197	198	4.771590	TGAGCATTGTGGAAATCAAGAC	57.228	40.909	0.00	0.00	0.00	3.01
223	224	2.832129	TCTCCACATCTTTTCTAGCCGT	59.168	45.455	0.00	0.00	0.00	5.68
274	275	3.027412	GAGCTGGTCCTCTCACAATAGA	58.973	50.000	0.00	0.00	0.00	1.98
409	410	1.226802	CTCGCACGGGATGTCTCAG	60.227	63.158	0.00	0.00	0.00	3.35
412	413	2.276116	ACACTCGCACGGGATGTCT	61.276	57.895	0.00	0.00	0.00	3.41
460	461	3.428532	GAATGGCATGATAGGAGGCAAT	58.571	45.455	0.00	0.00	41.29	3.56
484	485	0.248843	TCATCATGTGCTGCGGTACA	59.751	50.000	19.17	19.17	41.85	2.90
487	488	0.816825	GGATCATCATGTGCTGCGGT	60.817	55.000	0.00	0.00	0.00	5.68
495	496	8.260099	TGAGATTCTTCTAAGGATCATCATGT	57.740	34.615	12.48	0.00	42.45	3.21
506	507	6.985645	CCACTCCTCAATGAGATTCTTCTAAG	59.014	42.308	12.53	0.00	36.22	2.18
508	509	5.960811	ACCACTCCTCAATGAGATTCTTCTA	59.039	40.000	12.53	0.00	36.22	2.10
514	515	2.240667	CCCACCACTCCTCAATGAGATT	59.759	50.000	12.53	0.00	36.22	2.40
627	629	6.131544	ACTCAAGCAAACAGTTTATCGTTT	57.868	33.333	0.00	0.00	35.76	3.60
703	707	6.674694	ATGCATTACAAACACAAGCAAAAA	57.325	29.167	0.00	0.00	33.91	1.94
719	725	5.123027	TCTCGCACAAACAACATATGCATTA	59.877	36.000	3.54	0.00	36.02	1.90
844	867	4.469552	GCTAAAAATTAGTTTGTCGCCGT	58.530	39.130	0.00	0.00	0.00	5.68
1140	1179	1.455959	CGGGGGAGGACTTCTCGAT	60.456	63.158	0.00	0.00	43.34	3.59
1533	1572	2.280592	AACGACACACCCTTCGCC	60.281	61.111	0.00	0.00	38.88	5.54
1639	1678	0.877071	GGACACGTCGAACACCTCTA	59.123	55.000	0.00	0.00	0.00	2.43
1784	1823	2.045340	AACTGCATACCCGTGGGC	60.045	61.111	4.41	0.00	39.32	5.36
2196	3815	2.097825	AGATCAACAATCTTGGCCTGC	58.902	47.619	3.32	0.00	42.30	4.85
2395	4021	1.399714	TCTCCACAACACTCGACAGT	58.600	50.000	0.00	0.00	0.00	3.55
2401	4027	5.510520	GGATCTATCCATCTCCACAACACTC	60.511	48.000	4.04	0.00	46.38	3.51
2428	4055	9.719355	TCACTACAGCATCAGATAAAAGTAAAA	57.281	29.630	0.00	0.00	0.00	1.52
2429	4056	9.890629	ATCACTACAGCATCAGATAAAAGTAAA	57.109	29.630	0.00	0.00	0.00	2.01
2430	4057	9.534565	GATCACTACAGCATCAGATAAAAGTAA	57.465	33.333	0.00	0.00	0.00	2.24
2431	4058	8.918116	AGATCACTACAGCATCAGATAAAAGTA	58.082	33.333	0.00	0.00	0.00	2.24
2432	4059	7.790027	AGATCACTACAGCATCAGATAAAAGT	58.210	34.615	0.00	0.00	0.00	2.66
2433	4060	9.755804	TTAGATCACTACAGCATCAGATAAAAG	57.244	33.333	0.00	0.00	0.00	2.27
2551	4178	1.153745	GCAGTAGCGAGGGAGTGTG	60.154	63.158	0.00	0.00	0.00	3.82
2562	4189	4.629092	TCTTCTCATGATCATGCAGTAGC	58.371	43.478	27.68	0.00	38.65	3.58
2737	4364	7.692088	AGAGTTTGATTGAATGCTAGAAATCG	58.308	34.615	0.00	0.00	32.78	3.34
2865	4501	3.575805	TGTTTCAGGGCCTCTTTGATTT	58.424	40.909	0.95	0.00	0.00	2.17
3007	4661	8.397575	TGATAATAGTAGTCTGGTTAGAGCTG	57.602	38.462	0.00	0.00	32.48	4.24
3068	4722	1.171308	CAGTGATGAAGGCAACCCTG	58.829	55.000	0.00	0.00	41.90	4.45
3173	4827	3.129287	CAGAACACTGTGTTTGGAAGCTT	59.871	43.478	25.35	0.00	41.28	3.74
3312	4966	1.671742	GACTTCTGAAGGTGCCGGA	59.328	57.895	20.61	0.00	0.00	5.14

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.