AutoCloner

Multiple sequence alignment - TraesCS3D01G466800

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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	TraesCS3D01G466800	chr3D	100.000	3174	0	0	1	3174	570112836	570109663	0.000000e+00	5862.0
1	TraesCS3D01G466800	chr3D	88.462	1300	126	13	942	2229	567190645	567191932	0.000000e+00	1548.0
2	TraesCS3D01G466800	chr3A	93.139	2230	130	12	960	3174	702905030	702902809	0.000000e+00	3249.0
3	TraesCS3D01G466800	chr3A	88.231	1300	128	14	942	2229	701265134	701266420	0.000000e+00	1530.0
4	TraesCS3D01G466800	chr3A	81.664	769	114	11	997	1751	702915945	702915190	5.820000e-172	614.0
5	TraesCS3D01G466800	chr3A	76.599	1141	238	23	996	2118	655886368	655885239	4.530000e-168	601.0
6	TraesCS3D01G466800	chr3A	80.000	425	73	7	1773	2188	702915079	702914658	1.430000e-78	303.0
7	TraesCS3D01G466800	chrUn	99.823	1132	2	0	1	1132	352953879	352955010	0.000000e+00	2080.0
8	TraesCS3D01G466800	chrUn	88.454	1559	156	15	942	2490	40974011	40972467	0.000000e+00	1860.0
9	TraesCS3D01G466800	chrUn	75.386	1036	217	21	1074	2081	267761120	267762145	1.720000e-127	466.0
10	TraesCS3D01G466800	chr3B	88.846	1560	151	13	942	2492	756310738	756312283	0.000000e+00	1895.0
11	TraesCS3D01G466800	chr3B	85.906	596	81	3	1073	1666	756684364	756683770	1.610000e-177	632.0
12	TraesCS3D01G466800	chr3B	79.888	537	87	12	1657	2175	756682922	756682389	1.080000e-99	374.0
13	TraesCS3D01G466800	chr3B	71.311	488	117	20	2188	2659	794874217	794874697	1.560000e-18	104.0
14	TraesCS3D01G466800	chr3B	74.667	225	47	10	2263	2482	97718217	97717998	1.210000e-14	91.6
15	TraesCS3D01G466800	chr7A	92.569	794	46	6	1	791	665990400	665991183	0.000000e+00	1127.0
16	TraesCS3D01G466800	chr7A	92.453	530	32	1	1	530	646935400	646935921	0.000000e+00	750.0
17	TraesCS3D01G466800	chr7A	92.965	199	14	0	593	791	646935878	646936076	1.110000e-74	291.0
18	TraesCS3D01G466800	chr7A	95.395	152	7	0	792	943	646935969	646936120	3.160000e-60	243.0
19	TraesCS3D01G466800	chr7A	94.737	152	8	0	792	943	665991076	665991227	1.470000e-58	237.0
20	TraesCS3D01G466800	chr7A	84.444	90	11	3	854	943	253550624	253550710	5.640000e-13	86.1
21	TraesCS3D01G466800	chr5D	81.847	1256	193	16	942	2179	560926284	560925046	0.000000e+00	1024.0
22	TraesCS3D01G466800	chr2B	78.918	721	114	22	46	748	4488230	4487530	3.730000e-124	455.0
23	TraesCS3D01G466800	chr2B	72.070	512	124	15	2187	2686	708723762	708724266	5.520000e-28	135.0
24	TraesCS3D01G466800	chr1B	76.257	358	70	13	2188	2540	48734395	48734742	3.250000e-40	176.0
25	TraesCS3D01G466800	chr7D	96.364	55	2	0	889	943	600576627	600576573	1.210000e-14	91.6
26	TraesCS3D01G466800	chr7D	94.545	55	3	0	889	943	600621867	600621813	5.640000e-13	86.1
27	TraesCS3D01G466800	chr1D	93.443	61	4	0	883	943	33213043	33213103	1.210000e-14	91.6
28	TraesCS3D01G466800	chr7B	93.103	58	4	0	885	942	150682792	150682849	5.640000e-13	86.1
29	TraesCS3D01G466800	chr7B	91.525	59	5	0	885	943	39767281	39767223	7.300000e-12	82.4

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	TraesCS3D01G466800	chr3D	570109663	570112836	3173	True	5862.0	5862	100.000000	1	3174	1	chr3D.!!$R1	3173
1	TraesCS3D01G466800	chr3D	567190645	567191932	1287	False	1548.0	1548	88.462000	942	2229	1	chr3D.!!$F1	1287
2	TraesCS3D01G466800	chr3A	702902809	702905030	2221	True	3249.0	3249	93.139000	960	3174	1	chr3A.!!$R2	2214
3	TraesCS3D01G466800	chr3A	701265134	701266420	1286	False	1530.0	1530	88.231000	942	2229	1	chr3A.!!$F1	1287
4	TraesCS3D01G466800	chr3A	655885239	655886368	1129	True	601.0	601	76.599000	996	2118	1	chr3A.!!$R1	1122
5	TraesCS3D01G466800	chr3A	702914658	702915945	1287	True	458.5	614	80.832000	997	2188	2	chr3A.!!$R3	1191
6	TraesCS3D01G466800	chrUn	352953879	352955010	1131	False	2080.0	2080	99.823000	1	1132	1	chrUn.!!$F2	1131
7	TraesCS3D01G466800	chrUn	40972467	40974011	1544	True	1860.0	1860	88.454000	942	2490	1	chrUn.!!$R1	1548
8	TraesCS3D01G466800	chrUn	267761120	267762145	1025	False	466.0	466	75.386000	1074	2081	1	chrUn.!!$F1	1007
9	TraesCS3D01G466800	chr3B	756310738	756312283	1545	False	1895.0	1895	88.846000	942	2492	1	chr3B.!!$F1	1550
10	TraesCS3D01G466800	chr3B	756682389	756684364	1975	True	503.0	632	82.897000	1073	2175	2	chr3B.!!$R2	1102
11	TraesCS3D01G466800	chr7A	665990400	665991227	827	False	682.0	1127	93.653000	1	943	2	chr7A.!!$F3	942
12	TraesCS3D01G466800	chr7A	646935400	646936120	720	False	428.0	750	93.604333	1	943	3	chr7A.!!$F2	942
13	TraesCS3D01G466800	chr5D	560925046	560926284	1238	True	1024.0	1024	81.847000	942	2179	1	chr5D.!!$R1	1237
14	TraesCS3D01G466800	chr2B	4487530	4488230	700	True	455.0	455	78.918000	46	748	1	chr2B.!!$R1	702

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
1278	1293	0.450983	AGAACCTAGTCACGCTACGC	59.549	55.0	0.0	0.0	0.0	4.42	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2970	4167	0.106519	AGAATCCCCCTTTGATGCGG	60.107	55.0	0.0	0.0	0.0	5.69	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
1278	1293	0.450983	AGAACCTAGTCACGCTACGC	59.549	55.000	0.00	0.00	0.00	4.42
1407	1425	2.230664	TTGGCTCTCCAAGGTGTGT	58.769	52.632	0.00	0.00	46.89	3.72
1434	1467	1.645034	ACTGCTCGTTGGATTGATCG	58.355	50.000	0.00	0.00	0.00	3.69
1446	1480	6.456853	CGTTGGATTGATCGATTGCTTTTCTA	60.457	38.462	0.00	0.00	0.00	2.10
1496	1535	5.710646	TCTACAGGCTCCTGAAGATCTAAT	58.289	41.667	21.75	0.00	46.30	1.73
1519	1558	0.963962	GAACCAGATCCCGGCGTATA	59.036	55.000	6.01	0.00	0.00	1.47
1536	1575	5.408299	GGCGTATAACATTGATGAGCATACA	59.592	40.000	0.00	0.00	0.00	2.29
1579	1618	3.019564	GTCCTTCAGGCTTATGCACAAT	58.980	45.455	2.72	0.00	41.91	2.71
1587	1626	4.877823	CAGGCTTATGCACAATAGTTCAGA	59.122	41.667	2.72	0.00	41.91	3.27
1681	2582	4.483950	TGTAGGGAGGGATTCTGATGTAG	58.516	47.826	0.00	0.00	0.00	2.74
1709	2610	1.135257	CGAATTCTCTCACCTCTGCGT	60.135	52.381	3.52	0.00	0.00	5.24
1810	2806	1.135083	ACGCTGAGTATTTGACCTCCG	60.135	52.381	0.00	0.00	0.00	4.63
1814	2810	3.321111	GCTGAGTATTTGACCTCCGGATA	59.679	47.826	3.57	0.00	0.00	2.59
1833	2829	5.977129	CGGATATTTTGGTATGCTTTTGACC	59.023	40.000	0.00	0.00	0.00	4.02
1857	2853	4.219033	GGTGTAATCGACAAAGCAAAGTG	58.781	43.478	0.00	0.00	40.66	3.16
2051	3232	5.392767	TGAGCCGATAATAGTCCTTCATC	57.607	43.478	0.00	0.00	0.00	2.92
2091	3272	1.118965	TTCGTGAGGACCTTGGAGCA	61.119	55.000	0.00	0.00	0.00	4.26
2118	3299	2.564975	CTTGGAAGGCAGCTTGCG	59.435	61.111	0.00	0.00	46.21	4.85
2130	3316	1.394572	CAGCTTGCGATTCGAACATGA	59.605	47.619	10.88	0.00	0.00	3.07
2175	3364	1.661463	TCCCTCAAGAAGGCATGACT	58.339	50.000	0.00	0.00	44.71	3.41
2229	3421	3.368531	GGTGCCACGAAGATAGAGAGTTT	60.369	47.826	0.00	0.00	0.00	2.66
2256	3448	6.535150	GTGTCCTCACAGATTTGATATTTCGA	59.465	38.462	0.00	0.00	43.37	3.71
2354	3546	5.929415	ACGACATTTTGGTGAAGTTTTTGTT	59.071	32.000	0.00	0.00	0.00	2.83
2382	3574	2.693591	CGACCTGCACTTCTAGGGAATA	59.306	50.000	0.00	0.00	38.42	1.75
2502	3694	4.631377	GTGCATGTGAATGAGTAGCAGTAA	59.369	41.667	0.00	0.00	0.00	2.24
2503	3695	5.295292	GTGCATGTGAATGAGTAGCAGTAAT	59.705	40.000	0.00	0.00	0.00	1.89
2516	3708	1.369625	CAGTAATGTTGCTCCCGTCC	58.630	55.000	0.00	0.00	0.00	4.79
2519	3711	1.467342	GTAATGTTGCTCCCGTCCAAC	59.533	52.381	0.00	0.00	41.19	3.77
2553	3745	0.881118	TGAAGTCAAGGCGGCATTTC	59.119	50.000	13.08	3.87	0.00	2.17
2593	3785	5.640189	AGCATGGAGAAAATGTCTTCAAG	57.360	39.130	0.00	0.00	45.48	3.02
2633	3825	8.677148	TTCTTAGTTGTGAGAGCTATTTTGTT	57.323	30.769	0.00	0.00	0.00	2.83
2635	3827	9.944376	TCTTAGTTGTGAGAGCTATTTTGTTAT	57.056	29.630	0.00	0.00	0.00	1.89
2689	3884	8.193953	ACCTGTAATGGTTTTGAGAATGAATT	57.806	30.769	0.00	0.00	36.89	2.17
2742	3939	0.036010	CCGATGTGTCTCCCTGCTTT	60.036	55.000	0.00	0.00	0.00	3.51
2797	3994	0.398318	ACCTCCAGTTGCCTTGTCTC	59.602	55.000	0.00	0.00	0.00	3.36
2818	4015	3.118038	TCTGGCATCCTAATGGTTGGTAC	60.118	47.826	0.00	0.00	34.46	3.34
2824	4021	5.354792	GCATCCTAATGGTTGGTACGTTAAA	59.645	40.000	0.00	0.00	34.46	1.52
2830	4027	8.949177	CCTAATGGTTGGTACGTTAAACTTATT	58.051	33.333	0.00	5.04	0.00	1.40
2859	4056	6.993902	CCTTAACAGGTTTCAAAGTAGGTGTA	59.006	38.462	0.00	0.00	35.06	2.90
2911	4108	4.335416	CAATTAAGTTGGAAGAGGCCTCA	58.665	43.478	33.90	11.99	34.06	3.86
2952	4149	2.512515	GATGTGGCAGCGTCTCCC	60.513	66.667	0.00	0.00	0.00	4.30
2970	4167	1.303643	CTGGGTCCTTCAGGCCAAC	60.304	63.158	5.01	0.00	34.43	3.77
2979	4176	0.825425	TTCAGGCCAACCGCATCAAA	60.825	50.000	5.01	0.00	42.76	2.69
2983	4180	3.005540	GCCAACCGCATCAAAGGGG	62.006	63.158	0.00	0.00	46.27	4.79
2996	4193	2.097825	CAAAGGGGGATTCTGCTTCTG	58.902	52.381	0.00	0.00	0.00	3.02
3024	4221	8.902540	TTTGTTTCATATCTGTTGTCTGTAGT	57.097	30.769	0.00	0.00	0.00	2.73
3027	4224	9.990360	TGTTTCATATCTGTTGTCTGTAGTTTA	57.010	29.630	0.00	0.00	0.00	2.01
3036	4233	2.230508	TGTCTGTAGTTTAGCGACTGGG	59.769	50.000	0.00	0.00	0.00	4.45
3041	4238	1.302993	GTTTAGCGACTGGGGGCAA	60.303	57.895	0.00	0.00	0.00	4.52
3046	4243	2.429930	CGACTGGGGGCAAGAACA	59.570	61.111	0.00	0.00	0.00	3.18
3055	4252	2.557056	GGGGGCAAGAACAGTTTTCTAC	59.443	50.000	0.00	0.00	0.00	2.59
3068	4265	4.010349	AGTTTTCTACTGCTATTGCCACC	58.990	43.478	0.00	0.00	38.71	4.61
3074	4271	3.598019	ACTGCTATTGCCACCATTTTG	57.402	42.857	0.00	0.00	38.71	2.44
3092	4289	2.336945	TGGTTCTGCATGCCTGATAG	57.663	50.000	16.68	5.34	0.00	2.08
3097	4294	3.720193	GCATGCCTGATAGCGCGG	61.720	66.667	8.83	0.00	34.65	6.46
3114	4311	0.647410	CGGCTCAACTATGTGCTTCG	59.353	55.000	3.33	0.00	43.75	3.79
3167	4365	4.082733	GGTGTTCCCATGTTCTAGCTTTTC	60.083	45.833	0.00	0.00	0.00	2.29

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
1278	1293	0.739462	TGGTATCGTTGCTGCTTCGG	60.739	55.000	14.30	0.00	0.00	4.30
1398	1416	4.743493	AGCAGTTTTAAACACACACCTTG	58.257	39.130	10.60	0.00	0.00	3.61
1407	1425	5.066634	TCAATCCAACGAGCAGTTTTAAACA	59.933	36.000	10.60	0.00	42.02	2.83
1434	1467	8.865590	TTACAAAACCAACTAGAAAAGCAATC	57.134	30.769	0.00	0.00	0.00	2.67
1469	1504	3.295093	TCTTCAGGAGCCTGTAGAGATG	58.705	50.000	18.38	2.76	42.66	2.90
1496	1535	1.682451	CGCCGGGATCTGGTTCCTTA	61.682	60.000	2.18	0.00	35.97	2.69
1519	1558	4.275810	AGCCTTGTATGCTCATCAATGTT	58.724	39.130	0.00	0.00	32.41	2.71
1536	1575	0.690762	TAGGACGCCTTTCAAGCCTT	59.309	50.000	3.71	0.00	34.61	4.35
1551	1590	2.270434	AAGCCTGAAGGACCATAGGA	57.730	50.000	11.63	0.00	37.39	2.94
1608	1647	2.969821	TTTCTTTGGCCCTCAGCTTA	57.030	45.000	0.00	0.00	43.05	3.09
1681	2582	0.902531	TGAGAGAATTCGGGGGTGAC	59.097	55.000	0.00	0.00	0.00	3.67
1709	2610	5.238868	ACGCTTAGAATCTGAGCTACGAATA	59.761	40.000	21.91	0.00	40.30	1.75
1810	2806	5.977129	CGGTCAAAAGCATACCAAAATATCC	59.023	40.000	0.00	0.00	32.55	2.59
1814	2810	3.056179	CCCGGTCAAAAGCATACCAAAAT	60.056	43.478	0.00	0.00	32.55	1.82
1833	2829	1.434555	TGCTTTGTCGATTACACCCG	58.565	50.000	0.00	0.00	38.00	5.28
1857	2853	4.757149	ACACAGGCAAATAGAAAGAGTCAC	59.243	41.667	0.00	0.00	0.00	3.67
1926	2922	4.436584	GCATCTCAGTGATTGAAAACGAGG	60.437	45.833	7.26	0.00	34.81	4.63
2051	3232	5.007430	CGAATTCATCCATGACTTCTCCAAG	59.993	44.000	14.35	0.24	41.52	3.61
2118	3299	3.057596	TGGGCTTTTGTCATGTTCGAATC	60.058	43.478	0.00	0.00	0.00	2.52
2130	3316	0.673437	CATTGGTCGTGGGCTTTTGT	59.327	50.000	0.00	0.00	0.00	2.83
2175	3364	2.291153	ACTAGAGTAACCGGTGTGCCTA	60.291	50.000	8.52	7.35	0.00	3.93
2214	3406	4.158764	AGGACACCAAACTCTCTATCTTCG	59.841	45.833	0.00	0.00	0.00	3.79
2229	3421	5.698741	ATATCAAATCTGTGAGGACACCA	57.301	39.130	0.00	0.00	45.40	4.17
2354	3546	3.678056	AGAAGTGCAGGTCGTTGAATA	57.322	42.857	0.00	0.00	0.00	1.75
2382	3574	4.759205	GTGCTTGGGCCGGGGATT	62.759	66.667	2.18	0.00	37.74	3.01
2502	3694	0.606401	CAGTTGGACGGGAGCAACAT	60.606	55.000	0.00	0.00	35.94	2.71
2503	3695	1.227823	CAGTTGGACGGGAGCAACA	60.228	57.895	0.00	0.00	35.94	3.33
2512	3704	1.871080	AAAGAGACTGCAGTTGGACG	58.129	50.000	22.65	0.00	0.00	4.79
2513	3705	3.743396	CAGTAAAGAGACTGCAGTTGGAC	59.257	47.826	22.65	12.99	40.42	4.02
2516	3708	5.588568	CTTCAGTAAAGAGACTGCAGTTG	57.411	43.478	22.65	12.60	45.44	3.16
2519	3711	4.876125	TGACTTCAGTAAAGAGACTGCAG	58.124	43.478	13.48	13.48	45.44	4.41
2572	3764	5.633830	TCTTGAAGACATTTTCTCCATGC	57.366	39.130	0.00	0.00	31.02	4.06
2616	3808	9.283768	TCAAGAAATAACAAAATAGCTCTCACA	57.716	29.630	0.00	0.00	0.00	3.58
2633	3825	9.685276	TGCTTTGGATCTAAGATTCAAGAAATA	57.315	29.630	10.91	0.00	0.00	1.40
2635	3827	8.408043	TTGCTTTGGATCTAAGATTCAAGAAA	57.592	30.769	10.91	0.00	0.00	2.52
2647	3839	5.435686	ACAGGTACATTGCTTTGGATCTA	57.564	39.130	0.00	0.00	0.00	1.98
2715	3912	2.027469	GGGAGACACATCGGTTAACCTT	60.027	50.000	22.12	7.09	0.00	3.50
2717	3914	1.553704	AGGGAGACACATCGGTTAACC	59.446	52.381	15.13	15.13	0.00	2.85
2730	3927	4.331108	AGAAATCAAGAAAGCAGGGAGAC	58.669	43.478	0.00	0.00	0.00	3.36
2797	3994	2.442236	ACCAACCATTAGGATGCCAG	57.558	50.000	0.00	0.00	36.43	4.85
2818	4015	7.175410	CCTGTTAAGGCGTAATAAGTTTAACG	58.825	38.462	0.00	0.00	36.56	3.18
2859	4056	0.871163	GTTGCACTTGTGCATGCGTT	60.871	50.000	25.93	0.00	45.13	4.84
2911	4108	2.711547	AGACTGGCCTGAAAGTTACCTT	59.288	45.455	17.64	0.00	0.00	3.50
2952	4149	1.303643	GTTGGCCTGAAGGACCCAG	60.304	63.158	3.32	0.00	44.80	4.45
2970	4167	0.106519	AGAATCCCCCTTTGATGCGG	60.107	55.000	0.00	0.00	0.00	5.69
2979	4176	1.931007	GCCAGAAGCAGAATCCCCCT	61.931	60.000	0.00	0.00	42.97	4.79
2996	4193	6.088824	CAGACAACAGATATGAAACAAAGCC	58.911	40.000	0.00	0.00	0.00	4.35
3024	4221	1.002624	CTTGCCCCCAGTCGCTAAA	60.003	57.895	0.00	0.00	0.00	1.85
3027	4224	3.249189	TTCTTGCCCCCAGTCGCT	61.249	61.111	0.00	0.00	0.00	4.93
3046	4243	4.010349	GGTGGCAATAGCAGTAGAAAACT	58.990	43.478	0.00	0.00	44.61	2.66
3055	4252	2.896168	CCAAAATGGTGGCAATAGCAG	58.104	47.619	0.00	0.00	35.97	4.24
3068	4265	2.028839	TCAGGCATGCAGAACCAAAATG	60.029	45.455	21.36	2.19	0.00	2.32
3074	4271	0.950116	GCTATCAGGCATGCAGAACC	59.050	55.000	21.36	0.72	0.00	3.62
3092	4289	2.703409	CACATAGTTGAGCCGCGC	59.297	61.111	0.00	0.00	0.00	6.86
3097	4294	3.813529	AAACGAAGCACATAGTTGAGC	57.186	42.857	0.00	0.00	39.45	4.26
3128	4326	3.914426	ACACCCCACATACTTCATCTC	57.086	47.619	0.00	0.00	0.00	2.75
3153	4351	1.682087	GGGCCGGAAAAGCTAGAACAT	60.682	52.381	5.05	0.00	0.00	2.71

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.