AutoCloner

Multiple sequence alignment - TraesCS5D01G125700

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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	TraesCS5D01G125700	chr5D	100.000	3633	0	0	1	3633	192536792	192540424	0.000000e+00	6709.0
1	TraesCS5D01G125700	chr5D	80.405	592	112	4	1999	2588	201851171	201850582	7.160000e-122	448.0
2	TraesCS5D01G125700	chr5A	95.880	1529	55	6	1697	3223	230454047	230455569	0.000000e+00	2468.0
3	TraesCS5D01G125700	chr5A	98.003	751	10	2	938	1687	230453179	230453925	0.000000e+00	1299.0
4	TraesCS5D01G125700	chr5A	93.073	895	46	7	1	882	230452277	230453168	0.000000e+00	1295.0
5	TraesCS5D01G125700	chr5A	94.033	419	17	5	3222	3633	230455673	230456090	2.380000e-176	628.0
6	TraesCS5D01G125700	chr5A	82.047	596	103	4	1995	2588	225243112	225243705	4.190000e-139	505.0
7	TraesCS5D01G125700	chr5A	79.688	128	23	2	1771	1895	225242986	225243113	5.000000e-14	89.8
8	TraesCS5D01G125700	chr5B	95.730	1335	32	9	1704	3014	197193482	197192149	0.000000e+00	2126.0
9	TraesCS5D01G125700	chr5B	95.229	1048	35	5	658	1700	197201824	197200787	0.000000e+00	1644.0
10	TraesCS5D01G125700	chr5B	95.922	564	23	0	3070	3633	197191951	197191388	0.000000e+00	915.0
11	TraesCS5D01G125700	chr5B	81.681	595	98	5	1995	2588	212635546	212634962	5.450000e-133	484.0
12	TraesCS5D01G125700	chr5B	94.667	300	16	0	127	426	197204051	197203752	1.980000e-127	466.0
13	TraesCS5D01G125700	chr5B	95.833	216	9	0	457	672	197202054	197201839	2.080000e-92	350.0
14	TraesCS5D01G125700	chr5B	79.688	128	23	2	1771	1895	212635672	212635545	5.000000e-14	89.8
15	TraesCS5D01G125700	chr5B	97.619	42	1	0	421	462	197202114	197202073	5.030000e-09	73.1
16	TraesCS5D01G125700	chr4D	87.344	640	79	2	1995	2633	74159238	74158600	0.000000e+00	732.0
17	TraesCS5D01G125700	chr4B	87.188	640	80	2	1995	2633	106491961	106491323	0.000000e+00	726.0
18	TraesCS5D01G125700	chr4A	86.094	640	87	2	1995	2633	513805335	513805973	0.000000e+00	688.0
19	TraesCS5D01G125700	chr3A	83.114	533	86	3	1118	1648	651962412	651962942	1.960000e-132	483.0
20	TraesCS5D01G125700	chr3A	82.176	533	91	4	1118	1648	651648978	651649508	4.280000e-124	455.0
21	TraesCS5D01G125700	chr3D	82.331	532	92	2	1118	1648	516671486	516672016	9.190000e-126	460.0
22	TraesCS5D01G125700	chr3D	82.123	537	91	5	1115	1648	516855895	516856429	4.280000e-124	455.0
23	TraesCS5D01G125700	chr3B	82.331	532	92	2	1118	1648	680732611	680732081	9.190000e-126	460.0
24	TraesCS5D01G125700	chr3B	82.143	532	93	2	1118	1648	680477780	680477250	4.280000e-124	455.0
25	TraesCS5D01G125700	chr3B	82.176	533	91	4	1118	1648	680676742	680676212	4.280000e-124	455.0
26	TraesCS5D01G125700	chr2D	78.998	619	107	13	1995	2594	445060739	445061353	5.650000e-108	401.0
27	TraesCS5D01G125700	chr2B	76.151	478	82	20	2033	2482	359133942	359134415	4.720000e-54	222.0
28	TraesCS5D01G125700	chr1D	86.154	130	15	1	1766	1895	360467959	360468085	1.760000e-28	137.0
29	TraesCS5D01G125700	chr1B	86.154	130	15	1	1766	1895	482697690	482697816	1.760000e-28	137.0
30	TraesCS5D01G125700	chr1A	84.091	132	14	6	1766	1895	460281710	460281836	1.770000e-23	121.0
31	TraesCS5D01G125700	chr7B	100.000	28	0	0	2948	2975	671701354	671701327	7.000000e-03	52.8

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	TraesCS5D01G125700	chr5D	192536792	192540424	3632	False	6709.000	6709	100.00000	1	3633	1	chr5D.!!$F1	3632
1	TraesCS5D01G125700	chr5D	201850582	201851171	589	True	448.000	448	80.40500	1999	2588	1	chr5D.!!$R1	589
2	TraesCS5D01G125700	chr5A	230452277	230456090	3813	False	1422.500	2468	95.24725	1	3633	4	chr5A.!!$F2	3632
3	TraesCS5D01G125700	chr5A	225242986	225243705	719	False	297.400	505	80.86750	1771	2588	2	chr5A.!!$F1	817
4	TraesCS5D01G125700	chr5B	197191388	197193482	2094	True	1520.500	2126	95.82600	1704	3633	2	chr5B.!!$R1	1929
5	TraesCS5D01G125700	chr5B	197200787	197204051	3264	True	633.275	1644	95.83700	127	1700	4	chr5B.!!$R2	1573
6	TraesCS5D01G125700	chr5B	212634962	212635672	710	True	286.900	484	80.68450	1771	2588	2	chr5B.!!$R3	817
7	TraesCS5D01G125700	chr4D	74158600	74159238	638	True	732.000	732	87.34400	1995	2633	1	chr4D.!!$R1	638
8	TraesCS5D01G125700	chr4B	106491323	106491961	638	True	726.000	726	87.18800	1995	2633	1	chr4B.!!$R1	638
9	TraesCS5D01G125700	chr4A	513805335	513805973	638	False	688.000	688	86.09400	1995	2633	1	chr4A.!!$F1	638
10	TraesCS5D01G125700	chr3A	651962412	651962942	530	False	483.000	483	83.11400	1118	1648	1	chr3A.!!$F2	530
11	TraesCS5D01G125700	chr3A	651648978	651649508	530	False	455.000	455	82.17600	1118	1648	1	chr3A.!!$F1	530
12	TraesCS5D01G125700	chr3D	516671486	516672016	530	False	460.000	460	82.33100	1118	1648	1	chr3D.!!$F1	530
13	TraesCS5D01G125700	chr3D	516855895	516856429	534	False	455.000	455	82.12300	1115	1648	1	chr3D.!!$F2	533
14	TraesCS5D01G125700	chr3B	680732081	680732611	530	True	460.000	460	82.33100	1118	1648	1	chr3B.!!$R3	530
15	TraesCS5D01G125700	chr3B	680477250	680477780	530	True	455.000	455	82.14300	1118	1648	1	chr3B.!!$R1	530
16	TraesCS5D01G125700	chr3B	680676212	680676742	530	True	455.000	455	82.17600	1118	1648	1	chr3B.!!$R2	530
17	TraesCS5D01G125700	chr2D	445060739	445061353	614	False	401.000	401	78.99800	1995	2594	1	chr2D.!!$F1	599

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
860	2563	0.033601	TGGCCAAGAACACACCACTT	60.034	50.0	0.61	0.00	0.00	3.16	F
881	2585	0.244994	CCAGTCGTCAACTAGCTGCT	59.755	55.0	7.57	7.57	36.07	4.24	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2292	4116	0.456221	GAACTCGCGGGAGATGAAGA	59.544	55.000	33.29	0.0	43.27	2.87	R
2705	4544	5.003804	AGGTGCAATAACTAGGTTCAACAG	58.996	41.667	0.00	0.0	0.00	3.16	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
22	23	5.029807	TCCGTATGATGCAGGTCAAATAA	57.970	39.130	0.00	0.00	0.00	1.40
23	24	5.620206	TCCGTATGATGCAGGTCAAATAAT	58.380	37.500	0.00	0.00	0.00	1.28
32	33	5.639757	TGCAGGTCAAATAATGAATGAACG	58.360	37.500	0.00	0.00	40.50	3.95
41	44	9.743057	TCAAATAATGAATGAACGAAAACAGTT	57.257	25.926	0.00	0.00	34.30	3.16
55	58	6.113639	CGAAAACAGTTCAATTTCTTTTCGC	58.886	36.000	9.37	0.00	41.47	4.70
58	61	4.035017	ACAGTTCAATTTCTTTTCGCGTG	58.965	39.130	5.77	0.00	0.00	5.34
63	66	0.879090	ATTTCTTTTCGCGTGGGTCC	59.121	50.000	5.77	0.00	0.00	4.46
74	77	3.503839	TGGGTCCGGTTGGGCTTT	61.504	61.111	0.00	0.00	40.80	3.51
76	79	3.053896	GGTCCGGTTGGGCTTTCG	61.054	66.667	0.00	0.00	40.80	3.46
86	89	1.205820	GGGCTTTCGAAAACGTCCG	59.794	57.895	12.41	0.04	0.00	4.79
90	93	1.210870	CTTTCGAAAACGTCCGGTCA	58.789	50.000	12.41	0.00	0.00	4.02
94	97	2.211806	TCGAAAACGTCCGGTCAAAAT	58.788	42.857	0.00	0.00	0.00	1.82
224	227	0.320771	GGTTCACCGCTGACTGACAT	60.321	55.000	0.00	0.00	0.00	3.06
430	2076	4.291540	TGATTGGCAATAATGAAGACGC	57.708	40.909	13.65	0.00	0.00	5.19
592	2262	3.005684	GCAATCAACAAGGTGTTCCATGA	59.994	43.478	0.00	0.00	38.77	3.07
613	2283	7.280876	CCATGAGGTAGAAAGAAATCGAAATCA	59.719	37.037	0.00	0.00	0.00	2.57
617	2287	7.556844	AGGTAGAAAGAAATCGAAATCAGCTA	58.443	34.615	0.00	0.00	0.00	3.32
644	2314	4.464951	TGACGGTCATCTAAAGTACACCAT	59.535	41.667	6.76	0.00	0.00	3.55
656	2355	0.673333	TACACCATCACAGCTTGGCG	60.673	55.000	1.89	0.00	36.41	5.69
735	2434	0.248990	CGCACTGCAAAAGCAAGGAA	60.249	50.000	1.11	0.00	0.00	3.36
753	2452	5.753721	AGGAAGCTAGAATTCTCAACAGT	57.246	39.130	12.24	0.00	0.00	3.55
754	2453	6.859112	AGGAAGCTAGAATTCTCAACAGTA	57.141	37.500	12.24	0.00	0.00	2.74
831	2530	2.342650	CCATTTCCCCACACAGGCG	61.343	63.158	0.00	0.00	35.39	5.52
860	2563	0.033601	TGGCCAAGAACACACCACTT	60.034	50.000	0.61	0.00	0.00	3.16
876	2580	2.352814	CCACTTCCCAGTCGTCAACTAG	60.353	54.545	0.00	0.00	36.07	2.57
879	2583	0.888619	TCCCAGTCGTCAACTAGCTG	59.111	55.000	0.00	0.00	36.07	4.24
880	2584	0.737715	CCCAGTCGTCAACTAGCTGC	60.738	60.000	0.00	0.00	36.07	5.25
881	2585	0.244994	CCAGTCGTCAACTAGCTGCT	59.755	55.000	7.57	7.57	36.07	4.24
882	2586	1.472878	CCAGTCGTCAACTAGCTGCTA	59.527	52.381	9.34	9.34	36.07	3.49
883	2587	2.478709	CCAGTCGTCAACTAGCTGCTAG	60.479	54.545	29.91	29.91	39.72	3.42
884	2588	1.133407	AGTCGTCAACTAGCTGCTAGC	59.867	52.381	31.08	16.75	42.84	3.42
937	2641	1.064296	CGCGCCTAACTCGATCAGT	59.936	57.895	0.00	0.00	36.64	3.41
1692	3397	3.824443	CGGAACTCCAAACATACCCTTTT	59.176	43.478	0.00	0.00	35.14	2.27
1814	3638	2.574929	GTCGGTATCACGGCCACA	59.425	61.111	2.24	0.00	31.09	4.17
1922	3746	0.957395	AAAGCCATGACCGAGCTGTG	60.957	55.000	0.00	0.00	36.84	3.66
1945	3769	3.838120	TCTGCTCAGTGAGTGTAATTCG	58.162	45.455	21.06	2.28	31.39	3.34
1947	3771	3.575630	TGCTCAGTGAGTGTAATTCGTC	58.424	45.455	21.06	1.43	31.39	4.20
1964	3788	3.676540	TCGTCGTTTTGCTCTGTTTTTC	58.323	40.909	0.00	0.00	0.00	2.29
1965	3789	2.781646	CGTCGTTTTGCTCTGTTTTTCC	59.218	45.455	0.00	0.00	0.00	3.13
1967	3791	3.791353	GTCGTTTTGCTCTGTTTTTCCTG	59.209	43.478	0.00	0.00	0.00	3.86
1971	3795	0.944386	TGCTCTGTTTTTCCTGTCGC	59.056	50.000	0.00	0.00	0.00	5.19
1974	3798	2.483876	CTCTGTTTTTCCTGTCGCTGA	58.516	47.619	0.00	0.00	0.00	4.26
2292	4116	2.359107	CACATGGCCAGACAGCGT	60.359	61.111	13.05	0.00	0.00	5.07
2730	4569	5.935789	TGTTGAACCTAGTTATTGCACCTAC	59.064	40.000	0.00	0.00	0.00	3.18
2989	4847	8.079211	AGTGAGACTTAGGCATATCTTGTTTA	57.921	34.615	0.00	0.00	0.00	2.01
3042	4901	3.845781	TCAATGATTGAGACCTAGCCC	57.154	47.619	3.29	0.00	34.08	5.19
3050	4909	1.616628	AGACCTAGCCCCACCCAAG	60.617	63.158	0.00	0.00	0.00	3.61
3077	5078	1.722034	TCCTTGTGCCTCAGTTCTCT	58.278	50.000	0.00	0.00	0.00	3.10
3084	5085	2.999355	GTGCCTCAGTTCTCTTGACATC	59.001	50.000	0.00	0.00	0.00	3.06
3159	5160	6.757897	TCATGATAAAGACCCATTGTTGTC	57.242	37.500	0.00	0.00	0.00	3.18
3170	5171	4.078537	CCCATTGTTGTCTGAACCATACA	58.921	43.478	0.00	0.00	0.00	2.29
3205	5206	3.042887	GGTTCACTGAAATCAACGCAAC	58.957	45.455	0.00	0.00	0.00	4.17
3286	5392	5.448360	GCCTATGCTCTTGAGCTTACAAAAG	60.448	44.000	21.17	10.06	35.49	2.27
3362	5468	5.335689	CGTTTTTGAAACAAATAATTGCGGC	59.664	36.000	0.00	0.00	40.34	6.53
3372	5478	2.414058	TAATTGCGGCACACTGTTTG	57.586	45.000	0.05	0.00	0.00	2.93
3386	5492	6.092670	GCACACTGTTTGCAAGAGAATATCTA	59.907	38.462	13.65	0.00	37.23	1.98
3526	5633	3.138304	GCGCTCACATGGACCATTTATA	58.862	45.455	3.52	0.00	0.00	0.98

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
3	4	8.570488	TCATTCATTATTTGACCTGCATCATAC	58.430	33.333	0.00	0.00	32.84	2.39
5	6	7.591421	TCATTCATTATTTGACCTGCATCAT	57.409	32.000	0.00	0.00	32.84	2.45
22	23	8.647143	AAATTGAACTGTTTTCGTTCATTCAT	57.353	26.923	6.45	0.00	46.95	2.57
23	24	7.973388	AGAAATTGAACTGTTTTCGTTCATTCA	59.027	29.630	15.65	0.00	46.95	2.57
32	33	6.113639	CGCGAAAAGAAATTGAACTGTTTTC	58.886	36.000	0.00	0.00	32.85	2.29
41	44	1.950909	ACCCACGCGAAAAGAAATTGA	59.049	42.857	15.93	0.00	0.00	2.57
58	61	2.675423	GAAAGCCCAACCGGACCC	60.675	66.667	9.46	0.00	0.00	4.46
63	66	3.173247	GTTTTCGAAAGCCCAACCG	57.827	52.632	13.20	0.00	0.00	4.44
76	79	4.408694	CCATATTTTGACCGGACGTTTTC	58.591	43.478	9.46	0.00	0.00	2.29
119	122	8.032451	GGTTGCTCCTATCATCTACTAATTCTC	58.968	40.741	0.00	0.00	0.00	2.87
124	127	7.432148	TTTGGTTGCTCCTATCATCTACTAA	57.568	36.000	0.80	0.00	37.07	2.24
137	140	1.807226	GGCCGTATTTGGTTGCTCC	59.193	57.895	0.00	0.00	0.00	4.70
224	227	1.001974	CTCCGAGGTCAAACATGTCCA	59.998	52.381	0.00	0.00	0.00	4.02
430	2076	4.621991	AGACCCAATCATTTATCTCGTCG	58.378	43.478	0.00	0.00	0.00	5.12
592	2262	6.410540	AGCTGATTTCGATTTCTTTCTACCT	58.589	36.000	0.00	0.00	0.00	3.08
644	2314	0.608130	ACATAGTCGCCAAGCTGTGA	59.392	50.000	0.00	0.00	0.00	3.58
656	2355	5.539582	TGACGGCAAAACATAACATAGTC	57.460	39.130	0.00	0.00	0.00	2.59
735	2434	8.097038	TGAACATTACTGTTGAGAATTCTAGCT	58.903	33.333	8.25	0.00	45.57	3.32
753	2452	2.036006	GCGCCCCGTGTGAACATTA	61.036	57.895	0.00	0.00	0.00	1.90
754	2453	3.361977	GCGCCCCGTGTGAACATT	61.362	61.111	0.00	0.00	0.00	2.71
842	2541	0.668535	GAAGTGGTGTGTTCTTGGCC	59.331	55.000	0.00	0.00	0.00	5.36
860	2563	0.888619	CAGCTAGTTGACGACTGGGA	59.111	55.000	5.53	0.00	39.48	4.37
984	2689	3.376859	CCGCCATCACTTAAATTGTGCTA	59.623	43.478	0.00	0.00	35.58	3.49
1488	3193	2.435059	GAGCTCTTGCACGGGTCC	60.435	66.667	6.43	0.00	42.74	4.46
1814	3638	2.281070	CTGCGCCACACCTTCTGT	60.281	61.111	4.18	0.00	0.00	3.41
1922	3746	2.732412	TTACACTCACTGAGCAGAGC	57.268	50.000	5.92	0.00	35.28	4.09
1945	3769	3.791353	CAGGAAAAACAGAGCAAAACGAC	59.209	43.478	0.00	0.00	0.00	4.34
1947	3771	3.769536	ACAGGAAAAACAGAGCAAAACG	58.230	40.909	0.00	0.00	0.00	3.60
1964	3788	0.529337	CTATGCCAGTCAGCGACAGG	60.529	60.000	13.21	13.21	41.29	4.00
1965	3789	0.529337	CCTATGCCAGTCAGCGACAG	60.529	60.000	10.52	3.48	34.60	3.51
1967	3791	1.227380	CCCTATGCCAGTCAGCGAC	60.227	63.158	0.00	1.15	34.65	5.19
1971	3795	0.620556	AACACCCCTATGCCAGTCAG	59.379	55.000	0.00	0.00	0.00	3.51
1974	3798	1.282157	GAGAAACACCCCTATGCCAGT	59.718	52.381	0.00	0.00	0.00	4.00
1978	3802	1.559682	TCCTGAGAAACACCCCTATGC	59.440	52.381	0.00	0.00	0.00	3.14
2292	4116	0.456221	GAACTCGCGGGAGATGAAGA	59.544	55.000	33.29	0.00	43.27	2.87
2705	4544	5.003804	AGGTGCAATAACTAGGTTCAACAG	58.996	41.667	0.00	0.00	0.00	3.16
3039	4898	2.434336	GGATATTTTTCTTGGGTGGGGC	59.566	50.000	0.00	0.00	0.00	5.80
3042	4901	5.723295	CACAAGGATATTTTTCTTGGGTGG	58.277	41.667	0.00	0.00	41.35	4.61
3050	4909	5.904362	ACTGAGGCACAAGGATATTTTTC	57.096	39.130	0.00	0.00	0.00	2.29
3159	5160	7.927629	CCCCAAAATTATTCATGTATGGTTCAG	59.072	37.037	0.00	0.00	0.00	3.02
3170	5171	7.552050	TTCAGTGAACCCCAAAATTATTCAT	57.448	32.000	0.08	0.00	32.30	2.57
3205	5206	8.331022	CAAAACATCTAGTTGAGATTACGGATG	58.669	37.037	7.81	0.00	42.70	3.51
3362	5468	6.492007	AGATATTCTCTTGCAAACAGTGTG	57.508	37.500	0.00	0.00	0.00	3.82
3372	5478	8.924691	CACTTGCTAATCTAGATATTCTCTTGC	58.075	37.037	5.46	2.71	35.28	4.01
3386	5492	4.870021	AAGATTCCCCACTTGCTAATCT	57.130	40.909	0.00	0.00	38.27	2.40
3526	5633	6.147656	CCCGCAAAGAAAATAAAGAAAGCAAT	59.852	34.615	0.00	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.