AutoCloner

Multiple sequence alignment - TraesCS3A01G174300

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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	TraesCS3A01G174300	chr3A	100.000	2600	0	0	1	2600	192855212	192852613	0.000000e+00	4802.0
1	TraesCS3A01G174300	chr6D	90.265	2034	115	23	612	2599	133291280	133293276	0.000000e+00	2582.0
2	TraesCS3A01G174300	chr5B	87.957	2026	155	32	613	2580	673114955	673112961	0.000000e+00	2307.0
3	TraesCS3A01G174300	chr5A	87.692	2023	157	34	610	2573	364526140	364528129	0.000000e+00	2272.0
4	TraesCS3A01G174300	chr5A	81.275	251	41	2	1208	1452	244438410	244438160	5.680000e-47	198.0
5	TraesCS3A01G174300	chr5A	79.461	297	44	7	888	1184	244447328	244447049	7.340000e-46	195.0
6	TraesCS3A01G174300	chr4B	93.830	1491	42	12	1152	2598	28305164	28303680	0.000000e+00	2198.0
7	TraesCS3A01G174300	chr4B	91.878	394	13	11	613	991	28305564	28305175	1.370000e-147	532.0
8	TraesCS3A01G174300	chr1B	89.881	1176	73	16	613	1775	6347834	6348976	0.000000e+00	1471.0
9	TraesCS3A01G174300	chr1B	93.289	447	20	6	2161	2600	6349030	6349473	0.000000e+00	651.0
10	TraesCS3A01G174300	chrUn	95.098	612	21	5	1992	2598	278723915	278723308	0.000000e+00	955.0
11	TraesCS3A01G174300	chr3D	95.599	568	23	2	48	615	162181253	162180688	0.000000e+00	909.0
12	TraesCS3A01G174300	chr3D	98.214	56	1	0	1	56	162181650	162181595	5.920000e-17	99.0
13	TraesCS3A01G174300	chr3B	91.150	565	20	8	1666	2203	559206076	559206637	0.000000e+00	739.0
14	TraesCS3A01G174300	chr3B	96.143	363	12	1	2240	2600	559206628	559206990	2.230000e-165	592.0
15	TraesCS3A01G174300	chr3B	96.732	153	5	0	1	153	239252964	239252812	3.320000e-64	255.0
16	TraesCS3A01G174300	chr3B	93.529	170	10	1	446	615	239252732	239252564	4.300000e-63	252.0
17	TraesCS3A01G174300	chr3B	85.022	227	32	2	1139	1364	302347743	302347518	2.010000e-56	230.0
18	TraesCS3A01G174300	chr7D	85.714	476	40	6	1649	2100	397044	397515	6.510000e-131	477.0
19	TraesCS3A01G174300	chr7D	83.231	489	49	16	2123	2599	397566	398033	4.000000e-113	418.0
20	TraesCS3A01G174300	chr7D	76.763	241	25	14	2186	2421	34968534	34968320	3.540000e-19	106.0
21	TraesCS3A01G174300	chr6B	77.252	444	87	13	931	1368	1242121	1241686	5.560000e-62	248.0
22	TraesCS3A01G174300	chr6B	73.529	136	36	0	1013	1148	32596713	32596848	5.000000e-03	52.8
23	TraesCS3A01G174300	chr2B	85.903	227	30	2	1139	1364	3395397	3395622	9.300000e-60	241.0
24	TraesCS3A01G174300	chr2B	92.500	40	3	0	1109	1148	635044590	635044629	1.000000e-04	58.4
25	TraesCS3A01G174300	chr1D	81.457	151	24	3	1000	1146	451999961	451999811	1.260000e-23	121.0
26	TraesCS3A01G174300	chr7B	100.000	31	0	0	1118	1148	716257729	716257699	1.000000e-04	58.4

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	TraesCS3A01G174300	chr3A	192852613	192855212	2599	True	4802.0	4802	100.0000	1	2600	1	chr3A.!!$R1	2599
1	TraesCS3A01G174300	chr6D	133291280	133293276	1996	False	2582.0	2582	90.2650	612	2599	1	chr6D.!!$F1	1987
2	TraesCS3A01G174300	chr5B	673112961	673114955	1994	True	2307.0	2307	87.9570	613	2580	1	chr5B.!!$R1	1967
3	TraesCS3A01G174300	chr5A	364526140	364528129	1989	False	2272.0	2272	87.6920	610	2573	1	chr5A.!!$F1	1963
4	TraesCS3A01G174300	chr4B	28303680	28305564	1884	True	1365.0	2198	92.8540	613	2598	2	chr4B.!!$R1	1985
5	TraesCS3A01G174300	chr1B	6347834	6349473	1639	False	1061.0	1471	91.5850	613	2600	2	chr1B.!!$F1	1987
6	TraesCS3A01G174300	chrUn	278723308	278723915	607	True	955.0	955	95.0980	1992	2598	1	chrUn.!!$R1	606
7	TraesCS3A01G174300	chr3D	162180688	162181650	962	True	504.0	909	96.9065	1	615	2	chr3D.!!$R1	614
8	TraesCS3A01G174300	chr3B	559206076	559206990	914	False	665.5	739	93.6465	1666	2600	2	chr3B.!!$F1	934
9	TraesCS3A01G174300	chr7D	397044	398033	989	False	447.5	477	84.4725	1649	2599	2	chr7D.!!$F1	950

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
848	1215	0.806492	GACTGAATTCCGCTCGGGTC	60.806	60.0	8.59	3.24	37.0	4.46	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1942	2395	0.036952	CGTCATGTTCCTCTGCACCT	60.037	55.0	0.0	0.0	0.0	4.0	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
38	39	7.618502	TCATAAATATTGCCACGTTGTAACT	57.381	32.000	0.00	0.00	0.00	2.24
146	497	5.684704	TGGTTTATAGAGCAGATTCTTGGG	58.315	41.667	0.00	0.00	0.00	4.12
178	529	7.658179	ATGGCATGTTTACATACTCTTATCG	57.342	36.000	0.00	0.00	34.26	2.92
257	608	3.147629	CATCTTCAATGATGCCTCTCCC	58.852	50.000	0.00	0.00	37.59	4.30
321	672	3.838565	TCAAGACACCCAAATGGCTTTA	58.161	40.909	0.00	0.00	46.23	1.85
374	725	4.891992	TTCCTCTTGTAACTCTTGGGAG	57.108	45.455	0.00	0.00	44.62	4.30
405	756	9.933723	TTGGTTTATTGTAGTCTTACTCCTTAC	57.066	33.333	0.00	0.00	0.00	2.34
454	805	7.327214	AGACTGGCAAACTTGTTTTCATTTTA	58.673	30.769	0.00	0.00	0.00	1.52
455	806	7.821846	AGACTGGCAAACTTGTTTTCATTTTAA	59.178	29.630	0.00	0.00	0.00	1.52
480	831	3.165498	GCTTTCGTAGCCACACCG	58.835	61.111	1.58	0.00	44.48	4.94
527	878	6.983474	TTTATGTGTATGCGATATCATGGG	57.017	37.500	3.12	0.00	0.00	4.00
546	897	5.777850	TGGGCTTCTAAAACTTTTGTACC	57.222	39.130	0.00	0.00	0.00	3.34
587	938	9.814899	CATTAACACAGAGTTCTCAAGATATCT	57.185	33.333	0.00	0.00	41.64	1.98
591	942	6.593382	ACACAGAGTTCTCAAGATATCTTTGC	59.407	38.462	15.49	4.68	33.11	3.68
601	952	9.234827	TCTCAAGATATCTTTGCAGAAAATGAA	57.765	29.630	15.49	0.00	33.11	2.57
602	953	9.286946	CTCAAGATATCTTTGCAGAAAATGAAC	57.713	33.333	15.49	0.00	33.11	3.18
608	959	7.858052	ATCTTTGCAGAAAATGAACTTAACG	57.142	32.000	0.00	0.00	30.76	3.18
609	960	7.022055	TCTTTGCAGAAAATGAACTTAACGA	57.978	32.000	0.00	0.00	0.00	3.85
610	961	6.910433	TCTTTGCAGAAAATGAACTTAACGAC	59.090	34.615	0.00	0.00	0.00	4.34
620	971	8.623310	AAATGAACTTAACGACACGAAAATTT	57.377	26.923	0.00	0.00	0.00	1.82
759	1112	2.696707	ACGGGAAGAGACAGTTTGTACA	59.303	45.455	0.00	0.00	0.00	2.90
808	1161	1.083489	GACGGCCGTTTTCATCATGA	58.917	50.000	34.65	0.00	0.00	3.07
847	1214	1.218316	GACTGAATTCCGCTCGGGT	59.782	57.895	8.59	0.00	37.00	5.28
848	1215	0.806492	GACTGAATTCCGCTCGGGTC	60.806	60.000	8.59	3.24	37.00	4.46
849	1216	1.218047	CTGAATTCCGCTCGGGTCA	59.782	57.895	8.59	8.81	37.00	4.02
1029	1397	2.573009	TCTGAATCAAGGTGCTGATCCA	59.427	45.455	0.00	0.00	34.90	3.41
1045	1413	1.377725	CCAGCGGCACTTCCAATCT	60.378	57.895	1.45	0.00	34.01	2.40
1163	1531	6.701145	TGTAAGTGTCCAGTTTTTGCATAA	57.299	33.333	0.00	0.00	0.00	1.90
1240	1608	2.347114	CGTCAGGTGGTGGATGCA	59.653	61.111	0.00	0.00	0.00	3.96
1466	1843	1.068083	CAGGATACATGCTCGCCGT	59.932	57.895	0.00	0.00	41.41	5.68
1594	2012	1.207593	GTGGTCATGCACGTGCTTC	59.792	57.895	37.59	23.95	42.66	3.86
1664	2086	9.356433	TGCAAATCAAGTATTATGATGTTTGTG	57.644	29.630	0.00	0.00	37.58	3.33
1888	2311	3.334691	TCAAACTAACAGGATTCCAGCG	58.665	45.455	5.29	0.00	0.00	5.18
1912	2358	0.670546	GCACACATACAGGCGTCACT	60.671	55.000	0.00	0.00	0.00	3.41
1942	2395	0.252057	TACTGCTACCACTGCCCAGA	60.252	55.000	1.69	0.00	0.00	3.86
1960	2414	1.277557	AGAGGTGCAGAGGAACATGAC	59.722	52.381	0.00	0.00	0.00	3.06
1971	2425	2.744202	AGGAACATGACGTCAAGCAATC	59.256	45.455	24.13	16.18	0.00	2.67
1974	2428	3.044235	ACATGACGTCAAGCAATCTCA	57.956	42.857	24.13	0.00	0.00	3.27
2158	2643	4.133820	TCAAATCACAACGACAACCTGAT	58.866	39.130	0.00	0.00	0.00	2.90
2210	2702	8.726988	GGTTATTATTACAACAAGAGTCTTGCA	58.273	33.333	28.88	11.85	0.00	4.08
2268	2762	8.686334	ACACAGAACAAACACTGAATCTAAATT	58.314	29.630	0.00	0.00	37.54	1.82
2306	2800	3.016736	GCATTTGGCTCTAAGGTAGCAA	58.983	45.455	0.00	0.00	41.93	3.91
2467	2970	5.765182	CCCTGGTTCTCAACATATAATGGAC	59.235	44.000	0.00	0.00	33.60	4.02
2478	2981	5.670485	ACATATAATGGACAAGCGAGTTCA	58.330	37.500	0.00	0.00	33.60	3.18
2502	3009	1.271871	ACTTGTCCCGCATCCATTTCA	60.272	47.619	0.00	0.00	0.00	2.69

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
38	39	5.755409	TGAAACTTAGAGGGCTCACAATA	57.245	39.130	0.00	0.00	0.00	1.90
92	443	8.164070	AGGAACAGTTATAGGACAACTTTTCAT	58.836	33.333	13.19	6.13	41.34	2.57
146	497	3.199677	TGTAAACATGCCATACGGTAGC	58.800	45.455	0.00	0.00	33.28	3.58
178	529	1.376466	ACATGGAGTGTGGGAGCAC	59.624	57.895	0.00	0.00	40.28	4.40
248	599	4.749323	CAAGCATTGGGAGAGGCA	57.251	55.556	0.00	0.00	43.94	4.75
321	672	7.612677	ACTACGTAAGAAAATCAAGGATCTGT	58.387	34.615	0.00	0.00	43.62	3.41
405	756	3.388308	CCTCTTCAGGTATCGCTTCATG	58.612	50.000	0.00	0.00	34.60	3.07
507	858	3.054875	AGCCCATGATATCGCATACACAT	60.055	43.478	0.00	0.00	0.00	3.21
514	865	4.350368	TTTAGAAGCCCATGATATCGCA	57.650	40.909	0.00	0.00	0.00	5.10
525	876	6.401047	AAGGTACAAAAGTTTTAGAAGCCC	57.599	37.500	0.00	0.00	0.00	5.19
527	878	6.978659	AGCAAAGGTACAAAAGTTTTAGAAGC	59.021	34.615	0.00	0.00	0.00	3.86
569	920	7.040494	TCTGCAAAGATATCTTGAGAACTCTG	58.960	38.462	18.61	11.16	36.12	3.35
587	938	6.470877	GTGTCGTTAAGTTCATTTTCTGCAAA	59.529	34.615	0.00	0.00	0.00	3.68
591	942	5.969741	TCGTGTCGTTAAGTTCATTTTCTG	58.030	37.500	0.00	0.00	0.00	3.02
601	952	5.740099	CCAACAAATTTTCGTGTCGTTAAGT	59.260	36.000	0.00	0.00	0.00	2.24
602	953	5.331235	GCCAACAAATTTTCGTGTCGTTAAG	60.331	40.000	0.00	0.00	0.00	1.85
606	957	2.456010	GCCAACAAATTTTCGTGTCGT	58.544	42.857	0.00	0.00	0.00	4.34
607	958	1.446465	CGCCAACAAATTTTCGTGTCG	59.554	47.619	0.00	0.00	0.00	4.35
608	959	2.215363	CACGCCAACAAATTTTCGTGTC	59.785	45.455	10.46	0.00	41.33	3.67
609	960	2.189342	CACGCCAACAAATTTTCGTGT	58.811	42.857	10.46	0.00	41.33	4.49
610	961	1.520590	CCACGCCAACAAATTTTCGTG	59.479	47.619	11.30	11.30	44.50	4.35
620	971	3.858868	GAGCTCGTCCACGCCAACA	62.859	63.158	0.00	0.00	39.60	3.33
733	1084	2.282958	TGTCTCTTCCCGTCCGCT	60.283	61.111	0.00	0.00	0.00	5.52
808	1161	2.814805	AGCAGGGATACACATTGCTT	57.185	45.000	0.00	0.00	42.01	3.91
847	1214	5.546499	AGTTTAATGGAGTTGGTAGGTCTGA	59.454	40.000	0.00	0.00	0.00	3.27
848	1215	5.805728	AGTTTAATGGAGTTGGTAGGTCTG	58.194	41.667	0.00	0.00	0.00	3.51
849	1216	5.045797	GGAGTTTAATGGAGTTGGTAGGTCT	60.046	44.000	0.00	0.00	0.00	3.85
1029	1397	1.589716	GCAAGATTGGAAGTGCCGCT	61.590	55.000	0.00	0.00	40.66	5.52
1045	1413	0.034186	CCATAGTCCAGGCAAGGCAA	60.034	55.000	0.00	0.00	0.00	4.52
1163	1531	9.252962	GTGATGTTGAACAAATCTGAAGAAATT	57.747	29.630	0.62	0.00	0.00	1.82
1240	1608	3.305608	GCTTGCTGCCACTTGTAGAAATT	60.306	43.478	0.00	0.00	35.15	1.82
1664	2086	2.095059	CACTTGGCTGCTAACCAATGAC	60.095	50.000	0.00	0.00	45.84	3.06
1709	2131	0.250467	AGTTCGCCATCAGCAACACT	60.250	50.000	0.00	0.00	44.04	3.55
1793	2216	6.371825	ACACCTGCTTAGCTAAAAACATACTC	59.628	38.462	7.74	0.00	0.00	2.59
1888	2311	0.523968	CGCCTGTATGTGTGCAATGC	60.524	55.000	0.00	0.00	0.00	3.56
1900	2324	3.945981	TCAATACAAGTGACGCCTGTA	57.054	42.857	0.12	0.12	0.00	2.74
1901	2325	2.831685	TCAATACAAGTGACGCCTGT	57.168	45.000	0.00	0.00	0.00	4.00
1902	2326	4.685169	AATTCAATACAAGTGACGCCTG	57.315	40.909	0.00	0.00	0.00	4.85
1912	2358	6.093495	GCAGTGGTAGCAGTAATTCAATACAA	59.907	38.462	1.09	0.00	0.00	2.41
1942	2395	0.036952	CGTCATGTTCCTCTGCACCT	60.037	55.000	0.00	0.00	0.00	4.00
1960	2414	3.806521	CCCTCTTATGAGATTGCTTGACG	59.193	47.826	7.19	0.00	42.73	4.35
1971	2425	9.189156	TGATTTTATTTGTTCCCCTCTTATGAG	57.811	33.333	0.00	0.00	39.92	2.90
1974	2428	9.547279	AGTTGATTTTATTTGTTCCCCTCTTAT	57.453	29.630	0.00	0.00	0.00	1.73
2146	2631	2.912771	TGTTTGTGATCAGGTTGTCGT	58.087	42.857	0.00	0.00	0.00	4.34
2158	2643	2.029486	GTGAAGTACGCGTTGTTTGTGA	59.971	45.455	20.78	0.00	0.00	3.58
2210	2702	4.084380	GCGTTGTAGCCGTTAACTTTAACT	60.084	41.667	3.71	0.00	40.57	2.24
2231	2723	0.307760	GTTCTGTGTTGTTGAGGGCG	59.692	55.000	0.00	0.00	0.00	6.13
2268	2762	3.006323	AAATGCAATTTGCGGGTGACTTA	59.994	39.130	16.12	0.00	46.55	2.24
2306	2800	4.998051	AGGGTTGTACTCCATGTTGAAAT	58.002	39.130	9.22	0.00	0.00	2.17
2467	2970	4.378459	GGGACAAGTAAATGAACTCGCTTG	60.378	45.833	0.00	0.00	39.16	4.01
2478	2981	2.799126	TGGATGCGGGACAAGTAAAT	57.201	45.000	0.00	0.00	0.00	1.40
2502	3009	1.409790	TGACAGCAAATGCACAAGCTT	59.590	42.857	8.28	0.00	45.16	3.74

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.