AutoCloner

Multiple sequence alignment - TraesCS1D01G085100

Loading Multiple Alignment...

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	TraesCS1D01G085100	chr1D	100.000	2444	0	0	1	2444	69475505	69473062	0.000000e+00	4514.0
1	TraesCS1D01G085100	chr1D	97.168	459	13	0	110	568	69474043	69473585	0.000000e+00	776.0
2	TraesCS1D01G085100	chr1D	97.168	459	13	0	1463	1921	69475396	69474938	0.000000e+00	776.0
3	TraesCS1D01G085100	chr1D	85.207	169	16	4	1922	2084	99499911	99500076	5.410000e-37	165.0
4	TraesCS1D01G085100	chr1D	93.103	87	6	0	1922	2008	92323457	92323543	7.090000e-26	128.0
5	TraesCS1D01G085100	chr2D	94.334	1818	94	8	107	1921	217480923	217482734	0.000000e+00	2778.0
6	TraesCS1D01G085100	chr2D	93.612	1816	75	15	109	1921	317054124	317055901	0.000000e+00	2673.0
7	TraesCS1D01G085100	chr2D	92.429	1453	69	15	109	1558	317057320	317058734	0.000000e+00	2036.0
8	TraesCS1D01G085100	chr2D	96.141	1218	43	3	422	1636	292662680	292661464	0.000000e+00	1986.0
9	TraesCS1D01G085100	chr2D	91.839	821	42	13	649	1467	167766024	167766821	0.000000e+00	1122.0
10	TraesCS1D01G085100	chr2D	97.174	460	11	1	110	569	217482278	217482735	0.000000e+00	776.0
11	TraesCS1D01G085100	chr2D	95.207	459	22	0	1463	1921	217480927	217481385	0.000000e+00	726.0
12	TraesCS1D01G085100	chr2D	94.799	423	18	3	146	568	317055483	317055901	0.000000e+00	656.0
13	TraesCS1D01G085100	chr2D	93.028	459	12	2	1463	1921	317054125	317054563	0.000000e+00	652.0
14	TraesCS1D01G085100	chr2D	93.028	459	12	2	1463	1921	317057321	317057759	0.000000e+00	652.0
15	TraesCS1D01G085100	chr2D	97.188	320	9	0	1602	1921	317058739	317059058	2.140000e-150	542.0
16	TraesCS1D01G085100	chr2D	97.701	174	4	0	110	283	292661637	292661464	1.420000e-77	300.0
17	TraesCS1D01G085100	chr2D	94.186	172	10	0	112	283	292662832	292662661	1.860000e-66	263.0
18	TraesCS1D01G085100	chr3A	88.913	1840	163	17	109	1921	251144338	251146163	0.000000e+00	2230.0
19	TraesCS1D01G085100	chr3A	89.939	825	75	5	648	1470	26629848	26630666	0.000000e+00	1057.0
20	TraesCS1D01G085100	chr3A	87.667	300	36	1	1335	1634	184015035	184014737	5.000000e-92	348.0
21	TraesCS1D01G085100	chr5D	91.149	1062	38	10	863	1921	97051216	97052224	0.000000e+00	1389.0
22	TraesCS1D01G085100	chr5D	93.644	881	38	9	107	984	97050368	97051233	0.000000e+00	1301.0
23	TraesCS1D01G085100	chr5D	93.043	460	12	1	110	569	97051786	97052225	0.000000e+00	654.0
24	TraesCS1D01G085100	chr5D	95.349	172	8	0	110	281	481252177	481252348	8.610000e-70	274.0
25	TraesCS1D01G085100	chr5D	91.753	97	8	0	1	97	469403209	469403305	4.240000e-28	135.0
26	TraesCS1D01G085100	chr5A	88.517	1106	101	20	161	1252	60204285	60203192	0.000000e+00	1315.0
27	TraesCS1D01G085100	chr5A	87.648	421	36	13	1514	1921	60204285	60203868	2.200000e-130	475.0
28	TraesCS1D01G085100	chr7D	89.836	974	86	7	653	1623	14046636	14045673	0.000000e+00	1238.0
29	TraesCS1D01G085100	chr3B	89.058	987	102	3	649	1634	322010947	322011928	0.000000e+00	1219.0
30	TraesCS1D01G085100	chr3B	87.879	198	21	3	2247	2444	519860651	519860845	1.890000e-56	230.0
31	TraesCS1D01G085100	chr7B	86.327	980	114	15	648	1623	386694301	386693338	0.000000e+00	1050.0
32	TraesCS1D01G085100	chr7B	86.911	191	21	4	2253	2443	19273563	19273749	6.850000e-51	211.0
33	TraesCS1D01G085100	chr1B	93.858	521	30	2	1924	2444	103275582	103275064	0.000000e+00	784.0
34	TraesCS1D01G085100	chr1B	96.117	103	4	0	3	105	103275686	103275584	4.180000e-38	169.0
35	TraesCS1D01G085100	chr4D	94.886	176	9	0	110	285	441810804	441810979	2.390000e-70	276.0
36	TraesCS1D01G085100	chr2B	87.302	189	22	2	2255	2443	10767615	10767429	5.290000e-52	215.0
37	TraesCS1D01G085100	chr7A	86.458	192	24	2	2253	2444	55891379	55891568	2.460000e-50	209.0
38	TraesCS1D01G085100	chr6A	86.010	193	23	4	2253	2444	109177965	109177776	1.150000e-48	204.0
39	TraesCS1D01G085100	chr6A	90.566	53	5	0	2177	2229	377363162	377363214	1.210000e-08	71.3
40	TraesCS1D01G085100	chr4A	85.938	192	25	2	2253	2444	668155562	668155751	1.150000e-48	204.0
41	TraesCS1D01G085100	chr1A	86.631	187	22	3	2253	2438	434422678	434422862	1.150000e-48	204.0
42	TraesCS1D01G085100	chr6B	85.492	193	24	4	2253	2444	234148300	234148111	5.330000e-47	198.0
43	TraesCS1D01G085100	chr5B	89.691	97	10	0	1	97	576864677	576864773	9.180000e-25	124.0
44	TraesCS1D01G085100	chr3D	89.691	97	8	2	1	97	354963386	354963480	3.300000e-24	122.0

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	TraesCS1D01G085100	chr1D	69473062	69475505	2443	True	2022.000000	4514	98.112000	1	2444	3	chr1D.!!$R1	2443
1	TraesCS1D01G085100	chr2D	217480923	217482735	1812	False	1426.666667	2778	95.571667	107	1921	3	chr2D.!!$F2	1814
2	TraesCS1D01G085100	chr2D	317054124	317059058	4934	False	1201.833333	2673	94.014000	109	1921	6	chr2D.!!$F3	1812
3	TraesCS1D01G085100	chr2D	167766024	167766821	797	False	1122.000000	1122	91.839000	649	1467	1	chr2D.!!$F1	818
4	TraesCS1D01G085100	chr2D	292661464	292662832	1368	True	849.666667	1986	96.009333	110	1636	3	chr2D.!!$R1	1526
5	TraesCS1D01G085100	chr3A	251144338	251146163	1825	False	2230.000000	2230	88.913000	109	1921	1	chr3A.!!$F2	1812
6	TraesCS1D01G085100	chr3A	26629848	26630666	818	False	1057.000000	1057	89.939000	648	1470	1	chr3A.!!$F1	822
7	TraesCS1D01G085100	chr5D	97050368	97052225	1857	False	1114.666667	1389	92.612000	107	1921	3	chr5D.!!$F3	1814
8	TraesCS1D01G085100	chr5A	60203192	60204285	1093	True	895.000000	1315	88.082500	161	1921	2	chr5A.!!$R1	1760
9	TraesCS1D01G085100	chr7D	14045673	14046636	963	True	1238.000000	1238	89.836000	653	1623	1	chr7D.!!$R1	970
10	TraesCS1D01G085100	chr3B	322010947	322011928	981	False	1219.000000	1219	89.058000	649	1634	1	chr3B.!!$F1	985
11	TraesCS1D01G085100	chr7B	386693338	386694301	963	True	1050.000000	1050	86.327000	648	1623	1	chr7B.!!$R1	975
12	TraesCS1D01G085100	chr1B	103275064	103275686	622	True	476.500000	784	94.987500	3	2444	2	chr1B.!!$R1	2441

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
140	141	0.322366	GCCTGGCTGCTCTCTTTCTT	60.322	55.0	12.43	0.0	0.0	2.52	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1669	3738	0.031585	GGGATATGTGTACGCGCAGA	59.968	55.0	5.73	0.0	38.63	4.26	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
37	38	1.442769	CAAAGCAGCACATCCTACGT	58.557	50.000	0.00	0.00	0.00	3.57
73	74	3.310193	GGCCTTAGAGGACAGGATTAGT	58.690	50.000	0.00	0.00	45.15	2.24
140	141	0.322366	GCCTGGCTGCTCTCTTTCTT	60.322	55.000	12.43	0.00	0.00	2.52
142	143	2.512705	CCTGGCTGCTCTCTTTCTTTT	58.487	47.619	0.00	0.00	0.00	2.27
205	207	0.676782	CACGAGGATTTTTCCGGCCT	60.677	55.000	0.00	0.00	34.28	5.19
244	247	3.170127	CGCACGAACGCCCAAATA	58.830	55.556	0.00	0.00	0.00	1.40
341	356	1.865865	CGTACACATATCCCAGCACC	58.134	55.000	0.00	0.00	0.00	5.01
443	468	1.159713	ACATGCACGGCGTCCATATG	61.160	55.000	17.13	16.43	0.00	1.78
463	488	1.746615	ATGCGCGCATCAGTTCCTT	60.747	52.632	39.13	16.89	29.42	3.36
489	514	2.580601	GGCCACACGACCTGGTAGT	61.581	63.158	6.78	6.78	0.00	2.73
576	602	5.635120	AGATTATGCCTAACAATTCTCCCC	58.365	41.667	0.00	0.00	0.00	4.81
731	757	4.446413	GACCCGACCCGACGCATT	62.446	66.667	0.00	0.00	0.00	3.56
836	863	3.760035	GCTCCTTCTCCGTCGGCA	61.760	66.667	6.34	0.00	0.00	5.69
1374	1544	2.978010	CACACGGCCCGAAGCTTT	60.978	61.111	11.71	0.00	43.05	3.51
1533	3580	4.099266	CAGAGGTAGGAGAAAGGAGACATG	59.901	50.000	0.00	0.00	0.00	3.21
1558	3605	0.958382	CACGAGGATTTTTCCGGCCA	60.958	55.000	2.24	0.00	34.28	5.36
1561	3608	1.993369	GAGGATTTTTCCGGCCAGCG	61.993	60.000	2.24	0.00	34.28	5.18
1669	3738	6.341408	ACATCAGGTCTGGGGTTTTTATAT	57.659	37.500	0.00	0.00	0.00	0.86
1702	3771	2.105806	TATCCCAGCACACACGCACA	62.106	55.000	0.00	0.00	0.00	4.57
1921	5299	7.280876	TCTCATGTCAAAGATTATGCCTAACAC	59.719	37.037	0.00	0.00	0.00	3.32
1922	5300	7.112122	TCATGTCAAAGATTATGCCTAACACT	58.888	34.615	0.00	0.00	0.00	3.55
1942	5320	0.833287	CTGGTGACCTATCTGGGTGG	59.167	60.000	2.11	0.00	40.06	4.61
1975	5353	7.743749	AGCTTGATGTGGATATTCTATGTTCT	58.256	34.615	0.00	0.00	0.00	3.01
1984	5362	9.965902	GTGGATATTCTATGTTCTATTCCCAAT	57.034	33.333	0.00	0.00	0.00	3.16
2023	5401	2.537214	GGTATTTCGTCCGGATCGTTTC	59.463	50.000	20.62	2.33	0.00	2.78
2102	5480	2.926200	GCCATATATGTACAGCTGCTCG	59.074	50.000	15.27	0.00	0.00	5.03
2127	5505	1.062587	CTGTTCTAAGGGCGCATTTCG	59.937	52.381	10.83	0.00	42.12	3.46
2139	5517	3.789224	GGCGCATTTCGGTTATTTAACAG	59.211	43.478	10.83	0.00	37.92	3.16
2142	5520	3.789224	GCATTTCGGTTATTTAACAGGCG	59.211	43.478	3.12	0.00	37.92	5.52
2173	5551	6.101997	TCTTCATGCAGTGTGTAAGAGTATG	58.898	40.000	0.00	0.00	0.00	2.39
2193	5571	8.663209	AGTATGCAATCAGAACTCCTAGATAT	57.337	34.615	0.00	0.00	0.00	1.63
2216	5594	5.551760	AGAAATACAAGAGTTGCAATCCG	57.448	39.130	0.59	0.00	0.00	4.18
2221	5599	4.483476	ACAAGAGTTGCAATCCGTTTAC	57.517	40.909	0.59	0.00	0.00	2.01
2223	5601	4.024048	ACAAGAGTTGCAATCCGTTTACTG	60.024	41.667	0.59	0.00	0.00	2.74
2241	5619	4.587976	ACTGTAGGCTCTGTTAGGAGTA	57.412	45.455	0.00	0.00	35.89	2.59
2244	5622	6.063404	ACTGTAGGCTCTGTTAGGAGTATAC	58.937	44.000	0.00	0.00	35.89	1.47
2252	5630	7.769044	GGCTCTGTTAGGAGTATACAAATTGAA	59.231	37.037	5.50	0.00	35.89	2.69
2260	5638	5.753921	GGAGTATACAAATTGAACTCCCTCG	59.246	44.000	23.39	0.00	46.95	4.63
2264	5642	3.562182	ACAAATTGAACTCCCTCGGTTT	58.438	40.909	0.00	0.00	0.00	3.27
2278	5656	5.305902	TCCCTCGGTTTCATAATATAGTGCA	59.694	40.000	0.00	0.00	0.00	4.57
2399	5777	7.239763	TCACCACAAGATGTAGTTTCATAGA	57.760	36.000	0.00	0.00	0.00	1.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
57	58	5.706447	ACTATGCACTAATCCTGTCCTCTA	58.294	41.667	0.00	0.00	0.00	2.43
105	106	2.970324	GCTCGGCAACAACACGGA	60.970	61.111	0.00	0.00	0.00	4.69
140	141	2.229062	CTCTGTCCGTGAGTGAGCTAAA	59.771	50.000	0.00	0.00	0.00	1.85
142	143	1.454201	CTCTGTCCGTGAGTGAGCTA	58.546	55.000	0.00	0.00	0.00	3.32
244	247	3.794911	AGCCATTGGAAAGAGGGAAAAT	58.205	40.909	6.95	0.00	0.00	1.82
341	356	3.345011	TGATGTGTGCGTGCGTGG	61.345	61.111	0.00	0.00	0.00	4.94
576	602	4.202161	ACGACTAGCCATGTCAAGATTAGG	60.202	45.833	0.00	0.00	34.37	2.69
961	1109	4.662961	CGGTGAGCGTCTGGTGCA	62.663	66.667	0.00	0.00	33.85	4.57
1057	1217	2.817834	TATGCCGCCGTTGTGCTC	60.818	61.111	0.00	0.00	0.00	4.26
1070	1230	1.523938	GTTGGGAGGAGGCGTATGC	60.524	63.158	0.00	0.00	41.71	3.14
1487	3534	2.594321	CGTGAGTGAGCTGAGAGAAAG	58.406	52.381	0.00	0.00	0.00	2.62
1488	3535	1.270826	CCGTGAGTGAGCTGAGAGAAA	59.729	52.381	0.00	0.00	0.00	2.52
1533	3580	1.468914	GGAAAAATCCTCGTGTCCAGC	59.531	52.381	0.00	0.00	0.00	4.85
1589	3636	4.160329	GGAAAGAGGGAAAAGATTTGGGT	58.840	43.478	0.00	0.00	0.00	4.51
1669	3738	0.031585	GGGATATGTGTACGCGCAGA	59.968	55.000	5.73	0.00	38.63	4.26
1702	3771	2.032528	CAGGCCGGTGATGTGTGT	59.967	61.111	1.90	0.00	0.00	3.72
1921	5299	1.759445	CACCCAGATAGGTCACCAGAG	59.241	57.143	0.00	0.00	38.39	3.35
1922	5300	1.622449	CCACCCAGATAGGTCACCAGA	60.622	57.143	0.00	0.00	38.39	3.86
1942	5320	9.228949	AGAATATCCACATCAAGCTATTTCATC	57.771	33.333	0.00	0.00	0.00	2.92
1975	5353	0.546122	AGTGCTCGCCATTGGGAATA	59.454	50.000	4.53	0.00	35.59	1.75
2023	5401	4.813161	CACCAGCAACCATGATAGACTAAG	59.187	45.833	0.00	0.00	0.00	2.18
2057	5435	1.385743	CTCCTTCGTGCTTCGTTAACG	59.614	52.381	21.85	21.85	40.80	3.18
2061	5439	0.104304	ACACTCCTTCGTGCTTCGTT	59.896	50.000	0.00	0.00	38.45	3.85
2062	5440	0.597637	CACACTCCTTCGTGCTTCGT	60.598	55.000	0.00	0.00	38.45	3.85
2102	5480	1.923227	GCGCCCTTAGAACAGCAACC	61.923	60.000	0.00	0.00	0.00	3.77
2127	5505	5.587443	AGATACAACCGCCTGTTAAATAACC	59.413	40.000	1.13	0.00	34.69	2.85
2139	5517	1.331756	CTGCATGAAGATACAACCGCC	59.668	52.381	0.00	0.00	0.00	6.13
2142	5520	3.753272	ACACACTGCATGAAGATACAACC	59.247	43.478	8.02	0.00	0.00	3.77
2193	5571	6.170506	ACGGATTGCAACTCTTGTATTTCTA	58.829	36.000	0.00	0.00	0.00	2.10
2204	5582	4.092968	CCTACAGTAAACGGATTGCAACTC	59.907	45.833	0.00	0.50	0.00	3.01
2205	5583	4.000988	CCTACAGTAAACGGATTGCAACT	58.999	43.478	0.00	0.00	0.00	3.16
2213	5591	2.522185	ACAGAGCCTACAGTAAACGGA	58.478	47.619	0.00	0.00	0.00	4.69
2216	5594	5.185442	ACTCCTAACAGAGCCTACAGTAAAC	59.815	44.000	0.00	0.00	37.39	2.01
2221	5599	6.062749	TGTATACTCCTAACAGAGCCTACAG	58.937	44.000	4.17	0.00	37.39	2.74
2223	5601	6.956202	TTGTATACTCCTAACAGAGCCTAC	57.044	41.667	4.17	0.00	37.39	3.18
2241	5619	4.569719	ACCGAGGGAGTTCAATTTGTAT	57.430	40.909	0.00	0.00	0.00	2.29
2244	5622	3.568007	TGAAACCGAGGGAGTTCAATTTG	59.432	43.478	0.00	0.00	31.36	2.32
2252	5630	6.518537	GCACTATATTATGAAACCGAGGGAGT	60.519	42.308	0.00	0.00	0.00	3.85
2319	5697	9.665719	ATGTAAATGTTTTTCTCCACAAACTTT	57.334	25.926	0.00	0.00	34.52	2.66
2365	5743	8.489489	ACTACATCTTGTGGTGAATCTAATGAT	58.511	33.333	0.00	0.00	40.65	2.45

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.