AutoCloner

Multiple sequence alignment - TraesCS3D01G453700

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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	TraesCS3D01G453700	chr3D	100.000	2432	0	0	1	2432	560746184	560748615	0.000000e+00	4492
1	TraesCS3D01G453700	chr3D	96.977	827	23	2	1	826	173337652	173338477	0.000000e+00	1387
2	TraesCS3D01G453700	chr3D	87.287	999	108	8	827	1815	580118454	580119443	0.000000e+00	1123
3	TraesCS3D01G453700	chr3D	84.158	404	58	1	1302	1699	16585529	16585126	1.050000e-103	387
4	TraesCS3D01G453700	chr1D	97.333	825	22	0	1	825	395895533	395894709	0.000000e+00	1402
5	TraesCS3D01G453700	chr1D	96.871	831	23	3	1	829	234295347	234294518	0.000000e+00	1387
6	TraesCS3D01G453700	chr1D	96.977	827	24	1	1	826	373496580	373495754	0.000000e+00	1387
7	TraesCS3D01G453700	chr5D	96.973	826	24	1	1	825	51986378	51985553	0.000000e+00	1386
8	TraesCS3D01G453700	chr5D	87.269	1084	107	20	827	1890	453230722	453229650	0.000000e+00	1208
9	TraesCS3D01G453700	chr4D	96.973	826	23	2	1	825	310213862	310214686	0.000000e+00	1386
10	TraesCS3D01G453700	chr4D	96.977	827	22	3	1	825	465940775	465941600	0.000000e+00	1386
11	TraesCS3D01G453700	chr6D	96.751	831	25	2	1	829	449754433	449755263	0.000000e+00	1384
12	TraesCS3D01G453700	chr7D	96.519	833	27	2	1	832	471525497	471526328	0.000000e+00	1376
13	TraesCS3D01G453700	chr7D	87.814	1116	98	16	827	1918	457536256	457535155	0.000000e+00	1273
14	TraesCS3D01G453700	chr3B	88.246	1106	114	11	825	1918	10167067	10165966	0.000000e+00	1308
15	TraesCS3D01G453700	chr3B	82.797	1087	156	22	825	1891	661026566	661027641	0.000000e+00	942
16	TraesCS3D01G453700	chr3B	95.367	518	22	2	1915	2432	745245023	745245538	0.000000e+00	822
17	TraesCS3D01G453700	chr2B	87.365	1108	114	14	827	1918	492974259	492975356	0.000000e+00	1247
18	TraesCS3D01G453700	chr2B	82.473	1027	136	20	827	1837	118320871	118321869	0.000000e+00	859
19	TraesCS3D01G453700	chr2B	84.032	501	65	10	1431	1918	374456820	374457318	3.660000e-128	468
20	TraesCS3D01G453700	chr2B	87.915	331	34	1	1282	1606	374434119	374434449	3.790000e-103	385
21	TraesCS3D01G453700	chr6A	86.892	1007	108	14	827	1816	135451495	135450496	0.000000e+00	1107
22	TraesCS3D01G453700	chr1B	85.038	929	121	11	828	1743	452518763	452517840	0.000000e+00	929
23	TraesCS3D01G453700	chr1B	82.227	512	75	16	1393	1893	235509509	235509003	6.210000e-116	427
24	TraesCS3D01G453700	chrUn	95.367	518	22	2	1915	2432	201985194	201984679	0.000000e+00	822
25	TraesCS3D01G453700	chrUn	95.367	518	22	2	1915	2432	301716824	301716309	0.000000e+00	822
26	TraesCS3D01G453700	chr2D	92.007	588	38	3	825	1404	35334490	35335076	0.000000e+00	817
27	TraesCS3D01G453700	chr2D	86.486	333	31	9	1598	1918	35340600	35340930	1.070000e-93	353
28	TraesCS3D01G453700	chr1A	79.070	215	29	13	1667	1872	583249695	583249902	1.520000e-27	134

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	TraesCS3D01G453700	chr3D	560746184	560748615	2431	False	4492	4492	100.000	1	2432	1	chr3D.!!$F2	2431
1	TraesCS3D01G453700	chr3D	173337652	173338477	825	False	1387	1387	96.977	1	826	1	chr3D.!!$F1	825
2	TraesCS3D01G453700	chr3D	580118454	580119443	989	False	1123	1123	87.287	827	1815	1	chr3D.!!$F3	988
3	TraesCS3D01G453700	chr1D	395894709	395895533	824	True	1402	1402	97.333	1	825	1	chr1D.!!$R3	824
4	TraesCS3D01G453700	chr1D	234294518	234295347	829	True	1387	1387	96.871	1	829	1	chr1D.!!$R1	828
5	TraesCS3D01G453700	chr1D	373495754	373496580	826	True	1387	1387	96.977	1	826	1	chr1D.!!$R2	825
6	TraesCS3D01G453700	chr5D	51985553	51986378	825	True	1386	1386	96.973	1	825	1	chr5D.!!$R1	824
7	TraesCS3D01G453700	chr5D	453229650	453230722	1072	True	1208	1208	87.269	827	1890	1	chr5D.!!$R2	1063
8	TraesCS3D01G453700	chr4D	310213862	310214686	824	False	1386	1386	96.973	1	825	1	chr4D.!!$F1	824
9	TraesCS3D01G453700	chr4D	465940775	465941600	825	False	1386	1386	96.977	1	825	1	chr4D.!!$F2	824
10	TraesCS3D01G453700	chr6D	449754433	449755263	830	False	1384	1384	96.751	1	829	1	chr6D.!!$F1	828
11	TraesCS3D01G453700	chr7D	471525497	471526328	831	False	1376	1376	96.519	1	832	1	chr7D.!!$F1	831
12	TraesCS3D01G453700	chr7D	457535155	457536256	1101	True	1273	1273	87.814	827	1918	1	chr7D.!!$R1	1091
13	TraesCS3D01G453700	chr3B	10165966	10167067	1101	True	1308	1308	88.246	825	1918	1	chr3B.!!$R1	1093
14	TraesCS3D01G453700	chr3B	661026566	661027641	1075	False	942	942	82.797	825	1891	1	chr3B.!!$F1	1066
15	TraesCS3D01G453700	chr3B	745245023	745245538	515	False	822	822	95.367	1915	2432	1	chr3B.!!$F2	517
16	TraesCS3D01G453700	chr2B	492974259	492975356	1097	False	1247	1247	87.365	827	1918	1	chr2B.!!$F4	1091
17	TraesCS3D01G453700	chr2B	118320871	118321869	998	False	859	859	82.473	827	1837	1	chr2B.!!$F1	1010
18	TraesCS3D01G453700	chr6A	135450496	135451495	999	True	1107	1107	86.892	827	1816	1	chr6A.!!$R1	989
19	TraesCS3D01G453700	chr1B	452517840	452518763	923	True	929	929	85.038	828	1743	1	chr1B.!!$R2	915
20	TraesCS3D01G453700	chr1B	235509003	235509509	506	True	427	427	82.227	1393	1893	1	chr1B.!!$R1	500
21	TraesCS3D01G453700	chrUn	201984679	201985194	515	True	822	822	95.367	1915	2432	1	chrUn.!!$R1	517
22	TraesCS3D01G453700	chrUn	301716309	301716824	515	True	822	822	95.367	1915	2432	1	chrUn.!!$R2	517
23	TraesCS3D01G453700	chr2D	35334490	35335076	586	False	817	817	92.007	825	1404	1	chr2D.!!$F1	579

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
545	547	0.103572	GGCTGTTAGCGGGTTATCGA	59.896	55.0	0.0	0.0	43.62	3.59	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1692	1716	0.756294	TTGTCTTGCTTGGTCTCCGA	59.244	50.0	0.0	0.0	0.0	4.55	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
89	90	7.389607	GCCGTTAATGGGTATAAAGTGATACAT	59.610	37.037	15.60	0.00	34.50	2.29
141	142	2.350498	CGTTAATGGGCCAAGAGTTACG	59.650	50.000	11.89	11.16	0.00	3.18
238	239	1.522569	GGCCCAGATGACGCTACTT	59.477	57.895	0.00	0.00	0.00	2.24
387	389	2.250924	CTTTTCACAGGAATGGGCCTT	58.749	47.619	4.53	0.00	35.66	4.35
545	547	0.103572	GGCTGTTAGCGGGTTATCGA	59.896	55.000	0.00	0.00	43.62	3.59
733	735	7.507277	AGCACAGGTATGACTATCTTGATTCTA	59.493	37.037	0.00	0.00	0.00	2.10
864	867	2.607499	TGGCAACATGAATCCAAAGGT	58.393	42.857	0.00	0.00	46.17	3.50
1152	1166	3.708631	CAGATTTCTTCTCCTGCTCCCTA	59.291	47.826	0.00	0.00	29.93	3.53
1216	1230	7.065324	CCAATAAGAAACACACCGCTCTAAATA	59.935	37.037	0.00	0.00	0.00	1.40
1267	1281	5.551233	TCTGGAAACATAGAAGTTCCTGTG	58.449	41.667	8.91	4.37	41.51	3.66
1678	1702	3.766591	CCCGCTGGAGTATAGAAGATGAT	59.233	47.826	0.00	0.00	0.00	2.45
1692	1716	1.687660	AGATGATGATCTCGCAGCTGT	59.312	47.619	16.64	0.00	33.20	4.40
1719	1746	1.823470	AAGCAAGACAACTGCGCCA	60.823	52.632	4.18	0.00	0.00	5.69
1743	1770	1.630126	GGAGATCCCAGCCTGAGCAA	61.630	60.000	0.00	0.00	43.56	3.91
1744	1771	0.473326	GAGATCCCAGCCTGAGCAAT	59.527	55.000	0.00	0.00	43.56	3.56
1745	1772	0.183014	AGATCCCAGCCTGAGCAATG	59.817	55.000	0.00	0.00	43.56	2.82
1747	1774	2.923634	ATCCCAGCCTGAGCAATGCC	62.924	60.000	0.00	0.00	43.56	4.40
1749	1776	1.980232	CCAGCCTGAGCAATGCCAA	60.980	57.895	0.00	0.00	43.56	4.52
1750	1777	1.327690	CCAGCCTGAGCAATGCCAAT	61.328	55.000	0.00	0.00	43.56	3.16
1778	1816	4.065321	AGCCACTGTAATAGCTAGCTTG	57.935	45.455	24.88	12.90	32.73	4.01
1815	1856	7.951591	ACTGTAATAATGTGCACCTTCTTTTT	58.048	30.769	15.69	6.88	0.00	1.94
1817	1858	7.375053	TGTAATAATGTGCACCTTCTTTTTCC	58.625	34.615	15.69	0.88	0.00	3.13
1820	1867	0.679505	GTGCACCTTCTTTTTCCCCC	59.320	55.000	5.22	0.00	0.00	5.40
1837	1888	3.653836	TCCCCCTTACTGAACTTGCTTTA	59.346	43.478	0.00	0.00	0.00	1.85
1912	1970	3.403038	CGTTGGCCCTCCTATTATTCTG	58.597	50.000	0.00	0.00	0.00	3.02
1918	1976	5.891551	TGGCCCTCCTATTATTCTGAAAAAC	59.108	40.000	0.00	0.00	0.00	2.43
1919	1977	5.302059	GGCCCTCCTATTATTCTGAAAAACC	59.698	44.000	0.00	0.00	0.00	3.27
1936	1994	2.124277	ACCCTACGATTTTGCCTTCC	57.876	50.000	0.00	0.00	0.00	3.46
1941	1999	0.323629	ACGATTTTGCCTTCCTCCGA	59.676	50.000	0.00	0.00	0.00	4.55
1964	2022	1.139947	GGTAGCCGCTGAGAGTGTC	59.860	63.158	2.16	0.00	0.00	3.67
1965	2023	1.595993	GGTAGCCGCTGAGAGTGTCA	61.596	60.000	2.16	0.00	0.00	3.58
1977	2035	0.951040	GAGTGTCAACCTTGCTCCCG	60.951	60.000	0.00	0.00	0.00	5.14
2064	2122	6.072673	GCATATCTGCAATGTGAAGATCATGA	60.073	38.462	1.85	0.00	38.36	3.07
2066	2124	3.619929	TCTGCAATGTGAAGATCATGACG	59.380	43.478	0.00	0.00	23.62	4.35
2073	2131	4.578871	TGTGAAGATCATGACGGAAACAT	58.421	39.130	0.00	0.00	0.00	2.71
2113	2171	3.551046	CGTCGAGATAAGGAGGATGTTGG	60.551	52.174	0.00	0.00	0.00	3.77
2142	2200	5.005740	TCTTGAAACACCTCAATCTCCATG	58.994	41.667	0.00	0.00	34.86	3.66
2188	2246	6.893554	AGTCCACAAAAGTAAGGGTTTTAGTT	59.106	34.615	0.00	0.00	0.00	2.24
2256	2314	3.920412	GGCGTGTGATTGAGGAAAATTTC	59.080	43.478	0.00	0.00	0.00	2.17
2272	2330	8.869109	AGGAAAATTTCTTCACCATACAATTCA	58.131	29.630	5.65	0.00	0.00	2.57
2315	2373	1.144913	GGTGATGCTTAATGGCCCCTA	59.855	52.381	0.00	0.00	0.00	3.53
2343	2401	8.517878	CAGTTCTGAAATCAGGTTGTGATAATT	58.482	33.333	10.37	0.00	45.89	1.40
2355	2413	8.834465	CAGGTTGTGATAATTGAGGAATAAGAG	58.166	37.037	0.00	0.00	0.00	2.85
2361	2419	8.841300	GTGATAATTGAGGAATAAGAGGGTTTC	58.159	37.037	0.00	0.00	0.00	2.78

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
89	90	2.279935	AACTGGCCCGTAATGAACAA	57.720	45.000	0.00	0.00	0.00	2.83
141	142	2.194326	GCCCAGATGAGGCCCTTC	59.806	66.667	0.00	0.00	45.16	3.46
238	239	1.616865	CGACCTATCCGAATTAGGCCA	59.383	52.381	5.01	0.00	34.42	5.36
406	408	0.170561	GGCGCCTATGATACGTCGAT	59.829	55.000	22.15	0.00	0.00	3.59
545	547	0.330267	ATCGGGTCCGGTTTTGGATT	59.670	50.000	9.68	0.00	40.91	3.01
864	867	1.717032	AAGACCCAGCTGTGTACTCA	58.283	50.000	13.81	0.00	0.00	3.41
912	915	4.220602	ACTGAAGGAATGTAAATGGGTTGC	59.779	41.667	0.00	0.00	0.00	4.17
918	921	7.219484	AGACCAAACTGAAGGAATGTAAATG	57.781	36.000	0.00	0.00	0.00	2.32
1124	1138	5.568392	AGCAGGAGAAGAAATCTGAAACAT	58.432	37.500	0.00	0.00	38.96	2.71
1152	1166	4.689983	GCAATAGAAAGGTAATCAGCCCCT	60.690	45.833	0.00	0.00	0.00	4.79
1216	1230	6.239008	GCCCATAATACACATGCACAAATAGT	60.239	38.462	0.00	0.00	0.00	2.12
1669	1693	2.629137	AGCTGCGAGATCATCATCTTCT	59.371	45.455	0.00	0.00	39.71	2.85
1678	1702	1.997928	CTCCGACAGCTGCGAGATCA	61.998	60.000	25.33	8.26	0.00	2.92
1692	1716	0.756294	TTGTCTTGCTTGGTCTCCGA	59.244	50.000	0.00	0.00	0.00	4.55
1757	1794	3.742640	GCAAGCTAGCTATTACAGTGGCT	60.743	47.826	19.70	0.00	39.41	4.75
1758	1795	2.545946	GCAAGCTAGCTATTACAGTGGC	59.454	50.000	19.70	7.04	0.00	5.01
1778	1816	2.789409	ATTACAGTCCAAGGACCAGC	57.211	50.000	15.36	0.00	45.59	4.85
1815	1856	1.742308	AGCAAGTTCAGTAAGGGGGA	58.258	50.000	0.00	0.00	0.00	4.81
1817	1858	4.394729	TGTAAAGCAAGTTCAGTAAGGGG	58.605	43.478	0.00	0.00	0.00	4.79
1837	1888	3.877508	GAGTTCAGGTAACAACAGCTTGT	59.122	43.478	0.00	0.00	42.81	3.16
1865	1919	5.475564	CCCCTGGTTCCATTATTAATAACGG	59.524	44.000	13.08	13.08	0.00	4.44
1912	1970	4.514781	AGGCAAAATCGTAGGGTTTTTC	57.485	40.909	3.69	0.00	0.00	2.29
1918	1976	2.289565	GAGGAAGGCAAAATCGTAGGG	58.710	52.381	0.00	0.00	0.00	3.53
1919	1977	2.289565	GGAGGAAGGCAAAATCGTAGG	58.710	52.381	0.00	0.00	0.00	3.18
1954	2012	2.411904	GAGCAAGGTTGACACTCTCAG	58.588	52.381	0.00	0.00	0.00	3.35
1964	2022	1.002134	ATGGTCGGGAGCAAGGTTG	60.002	57.895	4.53	0.00	42.53	3.77
1965	2023	1.002134	CATGGTCGGGAGCAAGGTT	60.002	57.895	4.53	0.00	42.53	3.50
1977	2035	1.153549	GGTGGACGAGAGCATGGTC	60.154	63.158	17.19	17.19	36.00	4.02
2053	2111	4.831107	TCATGTTTCCGTCATGATCTTCA	58.169	39.130	0.00	0.00	44.14	3.02
2064	2122	2.233922	CACTAGGACCTCATGTTTCCGT	59.766	50.000	0.00	0.00	34.31	4.69
2066	2124	2.572104	ACCACTAGGACCTCATGTTTCC	59.428	50.000	0.00	0.00	38.69	3.13
2073	2131	1.632409	ACGTAGACCACTAGGACCTCA	59.368	52.381	0.00	0.00	37.74	3.86
2078	2136	1.827344	TCTCGACGTAGACCACTAGGA	59.173	52.381	0.00	0.00	37.74	2.94
2113	2171	3.194005	TGAGGTGTTTCAAGAGGTCAC	57.806	47.619	0.00	0.00	0.00	3.67
2130	2188	4.286291	TCCATCATCCTCATGGAGATTGAG	59.714	45.833	0.00	0.00	44.17	3.02
2142	2200	7.993183	TGGACTTTAACTTAATCCATCATCCTC	59.007	37.037	1.21	0.00	34.50	3.71
2194	2252	6.208402	GCAGGATTCATGTCTGAGTATAGAGA	59.792	42.308	0.00	0.00	31.68	3.10
2237	2295	6.642540	GGTGAAGAAATTTTCCTCAATCACAC	59.357	38.462	11.13	7.57	32.33	3.82
2272	2330	3.402681	CGAGTCCCCCATGCACCT	61.403	66.667	0.00	0.00	0.00	4.00
2315	2373	3.567164	CACAACCTGATTTCAGAACTGCT	59.433	43.478	9.15	0.00	46.59	4.24
2343	2401	7.178451	GGATTTTTGAAACCCTCTTATTCCTCA	59.822	37.037	0.00	0.00	0.00	3.86
2355	2413	6.866770	GCTAGTGTTTAGGATTTTTGAAACCC	59.133	38.462	0.00	0.00	32.06	4.11
2361	2419	7.672983	TCAGAGCTAGTGTTTAGGATTTTTG	57.327	36.000	0.00	0.00	0.00	2.44

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.