AutoCloner

Multiple sequence alignment - TraesCS4A01G345900

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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	TraesCS4A01G345900	chr4A	100.000	3305	0	0	1	3305	625078633	625075329	0.000000e+00	6104
1	TraesCS4A01G345900	chr4A	84.850	1934	234	39	603	2508	625166651	625164749	0.000000e+00	1893
2	TraesCS4A01G345900	chr4A	79.465	1047	190	18	1014	2043	624992940	624991902	0.000000e+00	719
3	TraesCS4A01G345900	chr4A	82.470	251	22	9	134	374	625167332	625167094	2.010000e-47	200
4	TraesCS4A01G345900	chr4A	74.645	422	97	7	1735	2149	625372439	625372021	9.420000e-41	178
5	TraesCS4A01G345900	chr5D	93.625	3341	150	20	1	3303	544230441	544233756	0.000000e+00	4931
6	TraesCS4A01G345900	chr5D	85.687	2096	234	34	434	2503	544148404	544150459	0.000000e+00	2148
7	TraesCS4A01G345900	chr5D	77.083	1152	244	15	1014	2151	544532515	544533660	0.000000e+00	647
8	TraesCS4A01G345900	chr5D	76.331	338	41	24	2694	3014	544150749	544151064	9.560000e-31	145
9	TraesCS4A01G345900	chr5D	95.312	64	2	1	134	197	544213589	544213651	2.100000e-17	100
10	TraesCS4A01G345900	chr5B	92.568	2368	134	27	947	3301	686432169	686434507	0.000000e+00	3360
11	TraesCS4A01G345900	chr5B	84.248	1949	241	47	596	2515	686200689	686202600	0.000000e+00	1838
12	TraesCS4A01G345900	chr5B	85.407	1350	108	42	343	1611	686333231	686334572	0.000000e+00	1319
13	TraesCS4A01G345900	chr5B	89.109	909	83	11	1609	2515	686342920	686343814	0.000000e+00	1116
14	TraesCS4A01G345900	chr5B	81.761	159	11	6	2694	2838	686202886	686203040	2.080000e-22	117
15	TraesCS4A01G345900	chr7B	79.381	291	54	4	1027	1313	1017580	1017868	2.010000e-47	200
16	TraesCS4A01G345900	chr5A	74.580	417	74	16	1742	2140	569544330	569543928	1.590000e-33	154
17	TraesCS4A01G345900	chr2B	86.441	118	14	2	1756	1872	390364316	390364200	9.630000e-26	128

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	TraesCS4A01G345900	chr4A	625075329	625078633	3304	True	6104.0	6104	100.0000	1	3305	1	chr4A.!!$R2	3304
1	TraesCS4A01G345900	chr4A	625164749	625167332	2583	True	1046.5	1893	83.6600	134	2508	2	chr4A.!!$R4	2374
2	TraesCS4A01G345900	chr4A	624991902	624992940	1038	True	719.0	719	79.4650	1014	2043	1	chr4A.!!$R1	1029
3	TraesCS4A01G345900	chr5D	544230441	544233756	3315	False	4931.0	4931	93.6250	1	3303	1	chr5D.!!$F2	3302
4	TraesCS4A01G345900	chr5D	544148404	544151064	2660	False	1146.5	2148	81.0090	434	3014	2	chr5D.!!$F4	2580
5	TraesCS4A01G345900	chr5D	544532515	544533660	1145	False	647.0	647	77.0830	1014	2151	1	chr5D.!!$F3	1137
6	TraesCS4A01G345900	chr5B	686432169	686434507	2338	False	3360.0	3360	92.5680	947	3301	1	chr5B.!!$F3	2354
7	TraesCS4A01G345900	chr5B	686333231	686334572	1341	False	1319.0	1319	85.4070	343	1611	1	chr5B.!!$F1	1268
8	TraesCS4A01G345900	chr5B	686342920	686343814	894	False	1116.0	1116	89.1090	1609	2515	1	chr5B.!!$F2	906
9	TraesCS4A01G345900	chr5B	686200689	686203040	2351	False	977.5	1838	83.0045	596	2838	2	chr5B.!!$F4	2242

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
780	1111	0.028902	GTCGGCAGACCACAACAAAC	59.971	55.0	5.6	0.0	41.41	2.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2489	2927	1.548269	GGTGCGGAAATTGAAATGGGA	59.452	47.619	0.0	0.0	0.0	4.37	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
490	536	0.601558	TGTGACAAGAGCCGTACCTC	59.398	55.000	0.00	0.00	0.00	3.85
535	595	9.543231	TCCTTTCTCTTACTCAATTTACCTCTA	57.457	33.333	0.00	0.00	0.00	2.43
559	619	1.195448	CATCCTGTCAACGACAAGCAC	59.805	52.381	0.00	0.00	42.26	4.40
578	643	0.319728	CTGATGGACTATGGCGGAGG	59.680	60.000	0.00	0.00	0.00	4.30
588	653	2.280592	GGCGGAGGTGTTCACGTT	60.281	61.111	0.00	0.00	0.00	3.99
591	666	1.219646	GCGGAGGTGTTCACGTTTAA	58.780	50.000	0.00	0.00	0.00	1.52
593	668	2.412325	GCGGAGGTGTTCACGTTTAATG	60.412	50.000	0.00	0.00	0.00	1.90
599	921	3.749609	GGTGTTCACGTTTAATGGCTACT	59.250	43.478	0.00	0.00	0.00	2.57
673	995	1.257750	GGGGGAAACATCCACAAGCC	61.258	60.000	0.00	0.00	34.04	4.35
722	1047	1.673920	GACAGCTAGAGTCGAGAAGGG	59.326	57.143	4.21	0.00	0.00	3.95
725	1050	0.753848	GCTAGAGTCGAGAAGGGGCT	60.754	60.000	4.21	0.00	0.00	5.19
780	1111	0.028902	GTCGGCAGACCACAACAAAC	59.971	55.000	5.60	0.00	41.41	2.93
1000	1394	1.341209	CATAGCATAGCAGACCACCGA	59.659	52.381	0.00	0.00	0.00	4.69
1045	1439	2.511145	GCCTGCTGCTCCTCTTCG	60.511	66.667	0.00	0.00	36.87	3.79
1333	1738	0.672401	GAACCATTTCGAGGGCGTCA	60.672	55.000	8.06	0.00	38.98	4.35
1363	1768	2.282958	TCTTCGGCCTCGTCAGGT	60.283	61.111	0.00	0.00	42.74	4.00
1583	1994	7.068103	GTCTCTTTCATCACTATCTTCTCTCCA	59.932	40.741	0.00	0.00	0.00	3.86
1659	2070	1.133253	CGACATGCCACTTCTTGCG	59.867	57.895	0.00	0.00	0.00	4.85
2313	2733	4.569719	AACCGGAGATTAATGACCTGTT	57.430	40.909	9.46	2.48	0.00	3.16
2486	2924	8.608844	AAGACCTTCTGTATCTTTACTGTTTG	57.391	34.615	0.00	0.00	28.03	2.93
2489	2927	9.654663	GACCTTCTGTATCTTTACTGTTTGTAT	57.345	33.333	0.00	0.00	0.00	2.29
2492	2930	9.099454	CTTCTGTATCTTTACTGTTTGTATCCC	57.901	37.037	0.00	0.00	0.00	3.85
2508	2946	3.525268	ATCCCATTTCAATTTCCGCAC	57.475	42.857	0.00	0.00	0.00	5.34
2532	3031	9.932207	CACCCATATTAGTATGTATTTCCGTAA	57.068	33.333	4.72	0.00	36.72	3.18
2802	3366	4.141274	TGGTTCATATACAGATGGGTTGGG	60.141	45.833	0.00	0.00	0.00	4.12
2820	3384	2.390427	GCGTTAGCATGTACCCACC	58.610	57.895	0.00	0.00	44.35	4.61
2821	3385	0.107848	GCGTTAGCATGTACCCACCT	60.108	55.000	0.00	0.00	44.35	4.00
2822	3386	1.651987	CGTTAGCATGTACCCACCTG	58.348	55.000	0.00	0.00	0.00	4.00
2823	3387	1.379527	GTTAGCATGTACCCACCTGC	58.620	55.000	0.00	0.00	44.10	4.85
2824	3388	0.988063	TTAGCATGTACCCACCTGCA	59.012	50.000	7.59	0.00	45.61	4.41
2825	3389	0.251916	TAGCATGTACCCACCTGCAC	59.748	55.000	7.59	0.00	45.61	4.57
2826	3390	2.398554	GCATGTACCCACCTGCACG	61.399	63.158	0.00	0.00	43.47	5.34
2827	3391	1.295101	CATGTACCCACCTGCACGA	59.705	57.895	0.00	0.00	0.00	4.35
2828	3392	0.740868	CATGTACCCACCTGCACGAG	60.741	60.000	0.00	0.00	0.00	4.18
2829	3393	2.434359	GTACCCACCTGCACGAGC	60.434	66.667	0.00	0.00	42.57	5.03
2830	3394	2.603473	TACCCACCTGCACGAGCT	60.603	61.111	6.36	0.00	42.74	4.09
2831	3395	2.942796	TACCCACCTGCACGAGCTG	61.943	63.158	6.36	5.51	42.74	4.24
2871	3435	2.314256	CGGAGGTACATGCATGCTG	58.686	57.895	26.53	16.29	0.00	4.41
2985	3566	5.163683	GCTGCAGAGAATCATTGCTTCTTTA	60.164	40.000	20.43	0.00	37.82	1.85
3036	3620	3.238441	CTCGTGCTTTCTCTCTGTGTAC	58.762	50.000	0.00	0.00	0.00	2.90
3052	3636	2.073056	TGTACGTGACATGAATGCACC	58.927	47.619	0.00	0.00	33.97	5.01
3072	3656	0.253044	TATGTCCTTGACTGGCTGCC	59.747	55.000	12.87	12.87	33.15	4.85
3087	3671	1.745087	GCTGCCGAGAATCATTTGGAA	59.255	47.619	0.00	0.00	33.17	3.53
3141	3725	0.321564	CACAACCGAGATGGCTCCAA	60.322	55.000	0.00	0.00	43.94	3.53
3158	3742	2.241176	TCCAAGATTACCGATTTGCCCT	59.759	45.455	0.00	0.00	0.00	5.19
3177	3762	1.588404	CTGCGAACGTATGTGGATCAC	59.412	52.381	0.00	0.00	34.56	3.06
3267	3852	1.696097	GGATGTGGGTCGGCCACTAT	61.696	60.000	9.07	0.00	38.79	2.12
3292	3877	6.102897	AGCTTACATGATATAGCGAGGTTT	57.897	37.500	0.00	0.00	38.62	3.27
3303	3888	1.001378	AGCGAGGTTTGACAATGCAAC	60.001	47.619	0.00	0.00	0.00	4.17
3304	3889	1.268999	GCGAGGTTTGACAATGCAACA	60.269	47.619	0.00	0.00	0.00	3.33

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
17	18	0.947244	CGCTTGTGTGGAGCTTTTCT	59.053	50.000	0.00	0.00	37.99	2.52
21	22	1.580845	GATGCGCTTGTGTGGAGCTT	61.581	55.000	9.73	0.00	37.99	3.74
22	23	2.033141	ATGCGCTTGTGTGGAGCT	59.967	55.556	9.73	0.00	37.99	4.09
28	29	0.462581	ATCATCGGATGCGCTTGTGT	60.463	50.000	13.15	0.00	30.86	3.72
323	338	2.019249	CCAACCGAGATGATGTGCATT	58.981	47.619	0.00	0.00	37.34	3.56
325	340	0.324614	ACCAACCGAGATGATGTGCA	59.675	50.000	0.00	0.00	0.00	4.57
490	536	1.948145	GAGATTCCCTCATGCAAGCAG	59.052	52.381	0.00	0.00	41.58	4.24
535	595	0.392706	TGTCGTTGACAGGATGCTGT	59.607	50.000	20.89	20.89	42.53	4.40
559	619	0.319728	CCTCCGCCATAGTCCATCAG	59.680	60.000	0.00	0.00	0.00	2.90
578	643	4.142966	GGAGTAGCCATTAAACGTGAACAC	60.143	45.833	0.00	0.00	36.34	3.32
599	921	1.076777	GGCATGGGCTAAAGCTGGA	60.077	57.895	1.39	0.00	41.70	3.86
673	995	0.830648	TTCGGCCCTAGTCCATCAAG	59.169	55.000	0.00	0.00	0.00	3.02
725	1050	1.136891	CATCGACTCATGGTGGCTACA	59.863	52.381	1.52	0.00	0.00	2.74
756	1087	2.737376	GTGGTCTGCCGACGGAAC	60.737	66.667	20.50	11.85	41.16	3.62
780	1111	3.077359	GACTCCCAGTTCAATCTTGGTG	58.923	50.000	0.00	0.00	0.00	4.17
1333	1738	1.388065	CCGAAGAGCTCGTCTGGGAT	61.388	60.000	24.22	0.00	46.65	3.85
1363	1768	0.824759	GCGAGGGAGAGCTTCCTTAA	59.175	55.000	12.71	0.00	45.98	1.85
1583	1994	3.777106	TGTTTCTGAGGTTGAGCTCAT	57.223	42.857	19.04	1.77	0.00	2.90
1659	2070	3.105937	GTTTGTGGAAAAGTCAAGCGAC	58.894	45.455	0.00	0.00	42.95	5.19
1887	2304	6.317642	TGTTAATGAAAACCATACCCGATGAG	59.682	38.462	0.00	0.00	37.82	2.90
2184	2604	2.365617	AGTATGGTTGCTCCCAGATACG	59.634	50.000	1.50	0.00	38.07	3.06
2486	2924	4.359706	GTGCGGAAATTGAAATGGGATAC	58.640	43.478	0.00	0.00	0.00	2.24
2489	2927	1.548269	GGTGCGGAAATTGAAATGGGA	59.452	47.619	0.00	0.00	0.00	4.37
2492	2930	2.739885	TGGGTGCGGAAATTGAAATG	57.260	45.000	0.00	0.00	0.00	2.32
2650	3149	4.080015	ACAAGGGATCATTCAACCGGATTA	60.080	41.667	9.46	0.00	0.00	1.75
2802	3366	0.107848	AGGTGGGTACATGCTAACGC	60.108	55.000	0.00	0.00	0.00	4.84
2831	3395	3.455469	GGGGGCTCATGCAAGTGC	61.455	66.667	7.42	7.42	41.91	4.40
2871	3435	3.191078	AGCCTGTCAAGTCATATGAGC	57.809	47.619	5.42	3.42	0.00	4.26
3036	3620	2.938451	ACATAGGTGCATTCATGTCACG	59.062	45.455	0.00	0.00	36.42	4.35
3052	3636	1.661341	GCAGCCAGTCAAGGACATAG	58.339	55.000	0.00	0.00	34.60	2.23
3072	3656	7.959689	ACTGAGATATTCCAAATGATTCTCG	57.040	36.000	0.00	0.00	31.46	4.04
3087	3671	0.833287	AGCGGCACCAACTGAGATAT	59.167	50.000	1.45	0.00	0.00	1.63
3141	3725	1.680338	GCAGGGCAAATCGGTAATCT	58.320	50.000	0.00	0.00	0.00	2.40
3158	3742	1.635844	GTGATCCACATACGTTCGCA	58.364	50.000	0.00	0.00	34.08	5.10
3177	3762	6.775088	AGTGTGTGTTGAATTATTGATAGCG	58.225	36.000	0.00	0.00	0.00	4.26
3267	3852	6.835819	ACCTCGCTATATCATGTAAGCTTA	57.164	37.500	0.86	0.86	32.73	3.09

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.