AutoCloner

Multiple sequence alignment - TraesCS6D01G362300

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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	TraesCS6D01G362300	chr6D	100.000	2840	0	0	1	2840	452932140	452929301	0.000000e+00	5245.0
1	TraesCS6D01G362300	chr6D	86.621	2205	245	29	236	2415	452848949	452851128	0.000000e+00	2392.0
2	TraesCS6D01G362300	chr6D	85.543	2089	264	19	236	2295	452906760	452908839	0.000000e+00	2150.0
3	TraesCS6D01G362300	chr6D	82.327	1573	227	27	684	2210	452841071	452842638	0.000000e+00	1317.0
4	TraesCS6D01G362300	chr6D	79.112	1599	278	35	658	2219	452484909	452483330	0.000000e+00	1051.0
5	TraesCS6D01G362300	chr6B	90.649	2481	151	28	236	2691	688125941	688123517	0.000000e+00	3221.0
6	TraesCS6D01G362300	chr6B	92.285	1672	110	10	948	2604	688064600	688062933	0.000000e+00	2355.0
7	TraesCS6D01G362300	chr6B	90.464	1552	100	8	673	2206	688033762	688032241	0.000000e+00	2002.0
8	TraesCS6D01G362300	chr6B	84.128	1405	192	14	913	2303	687956126	687957513	0.000000e+00	1330.0
9	TraesCS6D01G362300	chr6B	84.256	1264	180	9	963	2210	687732945	687734205	0.000000e+00	1214.0
10	TraesCS6D01G362300	chr6B	80.527	683	105	22	236	897	687955377	687956052	1.520000e-137	499.0
11	TraesCS6D01G362300	chr6B	81.583	619	90	16	331	934	687255264	687255873	9.140000e-135	490.0
12	TraesCS6D01G362300	chr6B	86.538	416	45	7	236	644	687874156	687874567	5.580000e-122	448.0
13	TraesCS6D01G362300	chr6B	85.965	399	51	4	236	633	687180007	687179613	3.380000e-114	422.0
14	TraesCS6D01G362300	chr6B	90.554	307	27	2	236	541	687959788	687960093	3.410000e-109	405.0
15	TraesCS6D01G362300	chr6B	93.562	233	15	0	1	233	688128674	688128442	5.820000e-92	348.0
16	TraesCS6D01G362300	chr6B	91.416	233	20	0	1	233	688081561	688081329	1.270000e-83	320.0
17	TraesCS6D01G362300	chr6B	87.047	193	8	2	2609	2784	688047198	688047006	4.800000e-48	202.0
18	TraesCS6D01G362300	chr6B	92.857	84	5	1	2701	2784	688123434	688123352	1.380000e-23	121.0
19	TraesCS6D01G362300	chr6B	100.000	45	0	0	888	932	688079655	688079611	1.810000e-12	84.2
20	TraesCS6D01G362300	chr6A	90.132	2118	166	21	236	2340	598926271	598924184	0.000000e+00	2713.0
21	TraesCS6D01G362300	chr6A	87.681	2208	230	27	236	2408	598810546	598812746	0.000000e+00	2532.0
22	TraesCS6D01G362300	chr6A	84.824	1364	187	8	958	2302	598860580	598861942	0.000000e+00	1354.0
23	TraesCS6D01G362300	chr6A	79.374	1566	282	27	678	2219	598156377	598154829	0.000000e+00	1064.0
24	TraesCS6D01G362300	chr6A	92.857	210	15	0	24	233	598927685	598927476	3.550000e-79	305.0
25	TraesCS6D01G362300	chr6A	87.045	247	28	4	652	896	598860219	598860463	2.790000e-70	276.0
26	TraesCS6D01G362300	chr2D	86.730	211	25	3	8	216	516627640	516627849	6.120000e-57	231.0
27	TraesCS6D01G362300	chr2D	85.185	216	27	5	3	216	574444842	574444630	1.710000e-52	217.0
28	TraesCS6D01G362300	chr1D	87.562	201	22	3	7	205	326903693	326903892	2.200000e-56	230.0
29	TraesCS6D01G362300	chr5D	85.714	210	26	4	14	220	495776935	495777143	4.760000e-53	219.0
30	TraesCS6D01G362300	chr2B	85.377	212	28	3	7	216	608359551	608359761	1.710000e-52	217.0
31	TraesCS6D01G362300	chr2B	82.105	190	28	6	2501	2688	559129430	559129615	1.050000e-34	158.0
32	TraesCS6D01G362300	chr3D	85.047	214	29	3	3	214	397915873	397916085	6.160000e-52	215.0
33	TraesCS6D01G362300	chr4A	82.632	190	29	4	2500	2688	368127667	368127481	6.290000e-37	165.0
34	TraesCS6D01G362300	chr3B	83.019	159	26	1	2515	2672	26519539	26519381	2.950000e-30	143.0
35	TraesCS6D01G362300	chr2A	83.761	117	16	3	2504	2618	617722102	617722217	1.080000e-19	108.0

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	TraesCS6D01G362300	chr6D	452929301	452932140	2839	True	5245.000000	5245	100.000000	1	2840	1	chr6D.!!$R2	2839
1	TraesCS6D01G362300	chr6D	452848949	452851128	2179	False	2392.000000	2392	86.621000	236	2415	1	chr6D.!!$F2	2179
2	TraesCS6D01G362300	chr6D	452906760	452908839	2079	False	2150.000000	2150	85.543000	236	2295	1	chr6D.!!$F3	2059
3	TraesCS6D01G362300	chr6D	452841071	452842638	1567	False	1317.000000	1317	82.327000	684	2210	1	chr6D.!!$F1	1526
4	TraesCS6D01G362300	chr6D	452483330	452484909	1579	True	1051.000000	1051	79.112000	658	2219	1	chr6D.!!$R1	1561
5	TraesCS6D01G362300	chr6B	688062933	688064600	1667	True	2355.000000	2355	92.285000	948	2604	1	chr6B.!!$R4	1656
6	TraesCS6D01G362300	chr6B	688032241	688033762	1521	True	2002.000000	2002	90.464000	673	2206	1	chr6B.!!$R2	1533
7	TraesCS6D01G362300	chr6B	688123352	688128674	5322	True	1230.000000	3221	92.356000	1	2784	3	chr6B.!!$R6	2783
8	TraesCS6D01G362300	chr6B	687732945	687734205	1260	False	1214.000000	1214	84.256000	963	2210	1	chr6B.!!$F2	1247
9	TraesCS6D01G362300	chr6B	687955377	687960093	4716	False	744.666667	1330	85.069667	236	2303	3	chr6B.!!$F4	2067
10	TraesCS6D01G362300	chr6B	687255264	687255873	609	False	490.000000	490	81.583000	331	934	1	chr6B.!!$F1	603
11	TraesCS6D01G362300	chr6B	688079611	688081561	1950	True	202.100000	320	95.708000	1	932	2	chr6B.!!$R5	931
12	TraesCS6D01G362300	chr6A	598810546	598812746	2200	False	2532.000000	2532	87.681000	236	2408	1	chr6A.!!$F1	2172
13	TraesCS6D01G362300	chr6A	598924184	598927685	3501	True	1509.000000	2713	91.494500	24	2340	2	chr6A.!!$R2	2316
14	TraesCS6D01G362300	chr6A	598154829	598156377	1548	True	1064.000000	1064	79.374000	678	2219	1	chr6A.!!$R1	1541
15	TraesCS6D01G362300	chr6A	598860219	598861942	1723	False	815.000000	1354	85.934500	652	2302	2	chr6A.!!$F2	1650

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
196	197	2.446802	GGCCCCCTTCCGAGATCT	60.447	66.667	0.0	0.0	0.0	2.75	F
941	3664	2.556622	GTCCTGCAATTTCTTTTCGGGA	59.443	45.455	0.0	0.0	0.0	5.14	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1038	3765	0.110056	GCCAGAAGCACATGAACACG	60.110	55.0	0.0	0.0	42.97	4.49	R
2645	6761	0.105964	TCAGCCATATACGGTGCCAC	59.894	55.0	0.0	0.0	0.00	5.01	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
68	69	3.075283	ACTTTGTACCCCATCCACAATCA	59.925	43.478	0.00	0.00	32.57	2.57
77	78	9.174166	GTACCCCATCCACAATCAATATTATAC	57.826	37.037	0.00	0.00	0.00	1.47
92	93	9.020731	TCAATATTATACGAGCAAGACATAGGA	57.979	33.333	0.00	0.00	0.00	2.94
133	134	2.453983	CGAACCCGGGTAAAACTGTA	57.546	50.000	30.52	0.00	0.00	2.74
196	197	2.446802	GGCCCCCTTCCGAGATCT	60.447	66.667	0.00	0.00	0.00	2.75
233	234	4.148825	CCGGCTTCTCCTCCACCG	62.149	72.222	0.00	0.00	43.44	4.94
234	235	3.068691	CGGCTTCTCCTCCACCGA	61.069	66.667	0.00	0.00	46.71	4.69
668	3240	4.512944	TCAATTCTCAAGTGTTGTGCTCTC	59.487	41.667	0.00	0.00	0.00	3.20
687	3266	6.026513	GCTCTCTTGCTACATTTGTGATTTC	58.973	40.000	0.00	0.00	0.00	2.17
941	3664	2.556622	GTCCTGCAATTTCTTTTCGGGA	59.443	45.455	0.00	0.00	0.00	5.14
1038	3765	1.599797	CGTGGGGGTGTTCTTGTCC	60.600	63.158	0.00	0.00	0.00	4.02
1133	3860	2.511600	CAACGGAGGCGTCATCCC	60.512	66.667	8.91	0.00	32.86	3.85
1209	3947	2.248248	TCGGAAGAGGAGCTCAAGAAA	58.752	47.619	17.19	0.00	34.84	2.52
1299	4041	2.711009	TCTGGAGGACAAGACCATTGTT	59.289	45.455	0.00	0.00	33.08	2.83
1404	4147	0.445436	GGAATGTCGTCAAGCTGCAG	59.555	55.000	10.11	10.11	0.00	4.41
1571	4314	1.626654	GCGCTGTCGTACATGCACTT	61.627	55.000	0.00	0.00	38.14	3.16
1789	4533	6.038271	GGACAAGAGTGATGTGTACAGTTTTT	59.962	38.462	0.00	0.00	0.00	1.94
1792	4536	4.275936	AGAGTGATGTGTACAGTTTTTGGC	59.724	41.667	0.00	0.00	0.00	4.52
1796	4540	1.671845	TGTGTACAGTTTTTGGCGTCC	59.328	47.619	0.00	0.00	0.00	4.79
2087	4837	3.971702	GGGGTCAGGCTGGTGCTT	61.972	66.667	15.73	0.00	39.59	3.91
2145	4909	6.775088	AGCAACAACGTGATGTGAATTATAG	58.225	36.000	0.00	0.00	32.81	1.31
2388	5867	6.542005	TCAACAACAGAAGAGAAATGCAACTA	59.458	34.615	0.00	0.00	0.00	2.24
2434	6545	6.152831	AGCAAAGACCAAAGGGATAAATACAC	59.847	38.462	0.00	0.00	38.05	2.90
2644	6760	8.758633	AATCCATATACATAAACTACGCTGAC	57.241	34.615	0.00	0.00	0.00	3.51
2669	6785	1.066454	CACCGTATATGGCTGACGTGA	59.934	52.381	11.13	0.00	34.81	4.35
2691	6807	1.000359	GGGGCCCACTTGTAGCAAT	60.000	57.895	26.86	0.00	0.00	3.56
2692	6808	0.614697	GGGGCCCACTTGTAGCAATT	60.615	55.000	26.86	0.00	0.00	2.32
2693	6809	1.266178	GGGCCCACTTGTAGCAATTT	58.734	50.000	19.95	0.00	0.00	1.82
2694	6810	1.623311	GGGCCCACTTGTAGCAATTTT	59.377	47.619	19.95	0.00	0.00	1.82
2695	6811	2.612721	GGGCCCACTTGTAGCAATTTTG	60.613	50.000	19.95	0.00	0.00	2.44
2696	6812	2.612721	GGCCCACTTGTAGCAATTTTGG	60.613	50.000	0.00	0.00	0.00	3.28
2699	6815	3.059166	CCACTTGTAGCAATTTTGGCAC	58.941	45.455	0.00	0.00	0.00	5.01
2749	7519	3.245264	CCACCTGTCAGGGGAACTAAAAT	60.245	47.826	23.64	0.00	43.10	1.82
2750	7520	3.758554	CACCTGTCAGGGGAACTAAAATG	59.241	47.826	23.06	4.26	43.10	2.32
2752	7522	4.105697	ACCTGTCAGGGGAACTAAAATGAA	59.894	41.667	23.06	0.00	40.58	2.57
2777	7547	1.154197	GTGCAAACCGGTCTCTAACC	58.846	55.000	8.04	0.00	45.45	2.85
2784	7554	2.404995	CGGTCTCTAACCCGCGACT	61.405	63.158	8.23	0.00	46.27	4.18
2785	7555	1.139095	GGTCTCTAACCCGCGACTG	59.861	63.158	8.23	0.00	42.85	3.51
2786	7556	1.139095	GTCTCTAACCCGCGACTGG	59.861	63.158	8.23	2.08	0.00	4.00
2787	7557	2.202756	CTCTAACCCGCGACTGGC	60.203	66.667	8.23	0.00	38.69	4.85
2798	7568	2.740055	GACTGGCGGAGTGTGCTG	60.740	66.667	0.00	0.00	33.83	4.41
2799	7569	4.320456	ACTGGCGGAGTGTGCTGG	62.320	66.667	0.00	0.00	31.75	4.85
2804	7574	4.007644	CGGAGTGTGCTGGCCTCA	62.008	66.667	3.32	0.00	0.00	3.86
2805	7575	2.431683	GGAGTGTGCTGGCCTCAA	59.568	61.111	3.32	0.00	0.00	3.02
2808	7578	0.321671	GAGTGTGCTGGCCTCAACTA	59.678	55.000	3.32	0.00	0.00	2.24
2835	7605	3.457610	TTTTTGAGGGTAACGACGACT	57.542	42.857	0.00	0.00	37.60	4.18
2836	7606	3.457610	TTTTGAGGGTAACGACGACTT	57.542	42.857	0.00	0.00	37.60	3.01
2837	7607	2.427232	TTGAGGGTAACGACGACTTG	57.573	50.000	0.00	0.00	37.60	3.16
2838	7608	0.599558	TGAGGGTAACGACGACTTGG	59.400	55.000	0.00	0.00	37.60	3.61
2839	7609	0.600057	GAGGGTAACGACGACTTGGT	59.400	55.000	0.00	0.00	37.60	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	9.961265	CTACCTTGTGATCGTATTAATGAGTTA	57.039	33.333	0.00	0.00	0.00	2.24
16	17	8.856103	TGATGATCTACCTTGTGATCGTATTAA	58.144	33.333	0.00	0.00	41.24	1.40
29	30	8.204836	GGTACAAAGTACATGATGATCTACCTT	58.795	37.037	0.00	0.00	0.00	3.50
77	78	5.360591	AGGTAAAATCCTATGTCTTGCTCG	58.639	41.667	0.00	0.00	35.87	5.03
120	121	5.737860	AGTAAAGGGATACAGTTTTACCCG	58.262	41.667	0.00	0.00	44.57	5.28
133	134	5.853572	TGGTTAACAGGAAGTAAAGGGAT	57.146	39.130	8.10	0.00	0.00	3.85
322	2867	1.480137	CTGATGAAGGCGGAGTTCTCT	59.520	52.381	0.00	0.00	0.00	3.10
395	2940	3.470567	GAAGACGCGGTCGCTGTG	61.471	66.667	12.47	0.74	37.67	3.66
668	3240	7.137490	TCAGAGAAATCACAAATGTAGCAAG	57.863	36.000	0.00	0.00	0.00	4.01
687	3266	7.884816	AAGCAATTTCAACATTTGATCAGAG	57.115	32.000	0.00	0.00	39.84	3.35
1038	3765	0.110056	GCCAGAAGCACATGAACACG	60.110	55.000	0.00	0.00	42.97	4.49
1172	3910	2.364324	TCCGAGAATATCTTGAACCCGG	59.636	50.000	0.00	0.00	36.14	5.73
1299	4041	3.009363	TCATCTTGGACTTCTTGATGGCA	59.991	43.478	0.00	0.00	36.24	4.92
1496	4239	1.507141	GAGTGCCTTGTTGGTGTCGG	61.507	60.000	0.00	0.00	38.35	4.79
1789	4533	1.654954	GCTCGAGTAGAAGGACGCCA	61.655	60.000	15.13	0.00	0.00	5.69
1792	4536	1.658994	AGAGCTCGAGTAGAAGGACG	58.341	55.000	15.13	0.00	0.00	4.79
1796	4540	3.181501	CCTGTCAAGAGCTCGAGTAGAAG	60.182	52.174	15.13	2.21	0.00	2.85
1888	4632	2.359478	CCGTGCCGGCCTACTTTT	60.359	61.111	26.77	0.00	41.17	2.27
2087	4837	0.764890	CTTTGCCCCTCATCCGGATA	59.235	55.000	18.63	5.05	0.00	2.59
2145	4909	1.300697	ACGTCTTGCGGTCTCAACC	60.301	57.895	0.00	0.00	46.52	3.77
2168	4933	8.280084	AGTGTATGTACTACCCTCTTCAAGATA	58.720	37.037	0.00	0.00	0.00	1.98
2357	5836	7.420002	CATTTCTCTTCTGTTGTTGAACATCA	58.580	34.615	8.60	8.60	41.33	3.07
2644	6760	1.069090	AGCCATATACGGTGCCACG	59.931	57.895	0.00	0.00	40.31	4.94
2645	6761	0.105964	TCAGCCATATACGGTGCCAC	59.894	55.000	0.00	0.00	0.00	5.01
2650	6766	1.066605	GTCACGTCAGCCATATACGGT	59.933	52.381	0.00	0.00	40.81	4.83
2669	6785	1.691219	CTACAAGTGGGCCCCATGT	59.309	57.895	22.27	22.73	35.28	3.21
2691	6807	9.313118	CGCATAGACATATATATAGTGCCAAAA	57.687	33.333	0.00	0.00	0.00	2.44
2692	6808	8.474831	ACGCATAGACATATATATAGTGCCAAA	58.525	33.333	0.00	0.00	0.00	3.28
2693	6809	8.007405	ACGCATAGACATATATATAGTGCCAA	57.993	34.615	0.00	0.00	0.00	4.52
2694	6810	7.582667	ACGCATAGACATATATATAGTGCCA	57.417	36.000	0.00	0.00	0.00	4.92
2695	6811	8.784994	ACTACGCATAGACATATATATAGTGCC	58.215	37.037	0.00	0.00	32.23	5.01
2696	6812	9.600646	CACTACGCATAGACATATATATAGTGC	57.399	37.037	0.00	1.89	30.42	4.40
2699	6815	8.237949	GCCCACTACGCATAGACATATATATAG	58.762	40.741	0.00	0.00	32.23	1.31
2749	7519	1.482593	ACCGGTTTGCACCATTTTTCA	59.517	42.857	0.00	0.00	44.53	2.69
2750	7520	2.131972	GACCGGTTTGCACCATTTTTC	58.868	47.619	9.42	0.00	44.53	2.29
2752	7522	1.339929	GAGACCGGTTTGCACCATTTT	59.660	47.619	9.42	0.00	44.53	1.82
2787	7557	3.535629	TTGAGGCCAGCACACTCCG	62.536	63.158	5.01	0.00	0.00	4.63
2788	7558	1.968540	GTTGAGGCCAGCACACTCC	60.969	63.158	5.01	0.00	0.00	3.85
2789	7559	0.321671	TAGTTGAGGCCAGCACACTC	59.678	55.000	5.01	0.00	0.00	3.51
2790	7560	0.322975	CTAGTTGAGGCCAGCACACT	59.677	55.000	5.01	11.16	0.00	3.55
2791	7561	0.674895	CCTAGTTGAGGCCAGCACAC	60.675	60.000	5.01	4.40	38.96	3.82
2792	7562	0.835971	TCCTAGTTGAGGCCAGCACA	60.836	55.000	5.01	0.00	46.25	4.57
2793	7563	0.391793	GTCCTAGTTGAGGCCAGCAC	60.392	60.000	5.01	0.00	46.25	4.40
2794	7564	0.545309	AGTCCTAGTTGAGGCCAGCA	60.545	55.000	5.01	0.00	46.25	4.41
2795	7565	0.615850	AAGTCCTAGTTGAGGCCAGC	59.384	55.000	5.01	0.00	46.25	4.85
2815	7585	3.457610	AGTCGTCGTTACCCTCAAAAA	57.542	42.857	0.00	0.00	0.00	1.94
2816	7586	3.125316	CAAGTCGTCGTTACCCTCAAAA	58.875	45.455	0.00	0.00	0.00	2.44
2817	7587	2.546373	CCAAGTCGTCGTTACCCTCAAA	60.546	50.000	0.00	0.00	0.00	2.69
2818	7588	1.000060	CCAAGTCGTCGTTACCCTCAA	60.000	52.381	0.00	0.00	0.00	3.02
2819	7589	0.599558	CCAAGTCGTCGTTACCCTCA	59.400	55.000	0.00	0.00	0.00	3.86
2820	7590	0.600057	ACCAAGTCGTCGTTACCCTC	59.400	55.000	0.00	0.00	0.00	4.30
2821	7591	2.737503	ACCAAGTCGTCGTTACCCT	58.262	52.632	0.00	0.00	0.00	4.34

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.