AutoCloner

Multiple sequence alignment - TraesCS4A01G133600

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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	TraesCS4A01G133600	chr4A	100.000	2647	0	0	1	2647	180835094	180837740	0.000000e+00	4889.0
1	TraesCS4A01G133600	chr4A	93.252	2386	112	18	1	2374	180843524	180845872	0.000000e+00	3469.0
2	TraesCS4A01G133600	chr4A	86.535	1010	109	24	4	996	319702569	319703568	0.000000e+00	1086.0
3	TraesCS4A01G133600	chr2A	89.351	1634	137	20	984	2600	528429165	528430778	0.000000e+00	2019.0
4	TraesCS4A01G133600	chr2A	91.137	1399	108	9	980	2374	528441490	528442876	0.000000e+00	1882.0
5	TraesCS4A01G133600	chr2A	91.202	1057	54	13	1256	2310	226616279	226615260	0.000000e+00	1400.0
6	TraesCS4A01G133600	chr2A	91.319	887	64	10	44	921	150132669	150133551	0.000000e+00	1199.0
7	TraesCS4A01G133600	chr2A	86.978	1006	104	24	5	996	284954532	284955524	0.000000e+00	1107.0
8	TraesCS4A01G133600	chr2A	87.277	951	105	14	6	945	528439095	528440040	0.000000e+00	1072.0
9	TraesCS4A01G133600	chr2A	86.081	467	40	6	1259	1725	226598221	226597780	1.840000e-131	479.0
10	TraesCS4A01G133600	chr2A	94.762	210	9	2	1723	1931	226593644	226593436	2.540000e-85	326.0
11	TraesCS4A01G133600	chr5A	92.509	1068	72	7	1311	2374	308626966	308628029	0.000000e+00	1522.0
12	TraesCS4A01G133600	chr5A	87.286	991	115	11	4	988	184323131	184322146	0.000000e+00	1122.0
13	TraesCS4A01G133600	chr5A	86.172	998	120	13	4	988	184331101	184330109	0.000000e+00	1062.0
14	TraesCS4A01G133600	chr5A	87.650	834	53	19	980	1805	308613651	308614442	0.000000e+00	924.0
15	TraesCS4A01G133600	chr5A	87.771	785	77	17	1817	2592	308614425	308615199	0.000000e+00	900.0
16	TraesCS4A01G133600	chr5A	85.324	293	18	5	980	1265	308626695	308626969	2.010000e-71	279.0
17	TraesCS4A01G133600	chr3A	90.728	1003	80	12	1	992	411096379	411097379	0.000000e+00	1325.0
18	TraesCS4A01G133600	chr3A	88.987	1017	85	19	1	996	411082499	411083509	0.000000e+00	1232.0
19	TraesCS4A01G133600	chr5B	87.069	812	93	10	1569	2374	39838469	39837664	0.000000e+00	907.0
20	TraesCS4A01G133600	chr7B	84.292	643	89	11	1967	2601	284918385	284919023	3.740000e-173	617.0
21	TraesCS4A01G133600	chr6A	81.869	717	115	14	1940	2647	305186042	305186752	8.160000e-165	590.0
22	TraesCS4A01G133600	chr6A	86.175	434	45	13	2165	2592	306588760	306588336	3.110000e-124	455.0
23	TraesCS4A01G133600	chr6A	80.076	527	74	29	2137	2647	367745456	367744945	1.940000e-96	363.0
24	TraesCS4A01G133600	chr6A	76.101	159	35	3	1550	1707	64878653	64878809	2.180000e-11	80.5
25	TraesCS4A01G133600	chr5D	83.478	460	66	9	2195	2647	138672027	138671571	1.130000e-113	420.0
26	TraesCS4A01G133600	chr7D	82.993	441	62	12	2215	2647	371642086	371641651	1.150000e-103	387.0
27	TraesCS4A01G133600	chr7D	77.594	665	130	18	1994	2647	406001409	406002065	4.130000e-103	385.0
28	TraesCS4A01G133600	chr2D	78.090	178	27	10	1809	1980	144823399	144823228	4.660000e-18	102.0
29	TraesCS4A01G133600	chr4D	71.625	363	84	18	1414	1767	320852133	320851781	6.070000e-12	82.4
30	TraesCS4A01G133600	chr1A	78.814	118	16	9	1415	1527	529907434	529907321	1.310000e-08	71.3
31	TraesCS4A01G133600	chr1A	84.848	66	4	3	966	1025	413746384	413746319	7.910000e-06	62.1
32	TraesCS4A01G133600	chr1A	83.871	62	8	2	966	1025	413735121	413735060	1.020000e-04	58.4
33	TraesCS4A01G133600	chr2B	97.297	37	1	0	988	1024	785959730	785959694	2.200000e-06	63.9

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	TraesCS4A01G133600	chr4A	180835094	180837740	2646	False	4889.0	4889	100.0000	1	2647	1	chr4A.!!$F1	2646
1	TraesCS4A01G133600	chr4A	180843524	180845872	2348	False	3469.0	3469	93.2520	1	2374	1	chr4A.!!$F2	2373
2	TraesCS4A01G133600	chr4A	319702569	319703568	999	False	1086.0	1086	86.5350	4	996	1	chr4A.!!$F3	992
3	TraesCS4A01G133600	chr2A	528429165	528430778	1613	False	2019.0	2019	89.3510	984	2600	1	chr2A.!!$F3	1616
4	TraesCS4A01G133600	chr2A	528439095	528442876	3781	False	1477.0	1882	89.2070	6	2374	2	chr2A.!!$F4	2368
5	TraesCS4A01G133600	chr2A	226615260	226616279	1019	True	1400.0	1400	91.2020	1256	2310	1	chr2A.!!$R3	1054
6	TraesCS4A01G133600	chr2A	150132669	150133551	882	False	1199.0	1199	91.3190	44	921	1	chr2A.!!$F1	877
7	TraesCS4A01G133600	chr2A	284954532	284955524	992	False	1107.0	1107	86.9780	5	996	1	chr2A.!!$F2	991
8	TraesCS4A01G133600	chr5A	184322146	184323131	985	True	1122.0	1122	87.2860	4	988	1	chr5A.!!$R1	984
9	TraesCS4A01G133600	chr5A	184330109	184331101	992	True	1062.0	1062	86.1720	4	988	1	chr5A.!!$R2	984
10	TraesCS4A01G133600	chr5A	308613651	308615199	1548	False	912.0	924	87.7105	980	2592	2	chr5A.!!$F1	1612
11	TraesCS4A01G133600	chr5A	308626695	308628029	1334	False	900.5	1522	88.9165	980	2374	2	chr5A.!!$F2	1394
12	TraesCS4A01G133600	chr3A	411096379	411097379	1000	False	1325.0	1325	90.7280	1	992	1	chr3A.!!$F2	991
13	TraesCS4A01G133600	chr3A	411082499	411083509	1010	False	1232.0	1232	88.9870	1	996	1	chr3A.!!$F1	995
14	TraesCS4A01G133600	chr5B	39837664	39838469	805	True	907.0	907	87.0690	1569	2374	1	chr5B.!!$R1	805
15	TraesCS4A01G133600	chr7B	284918385	284919023	638	False	617.0	617	84.2920	1967	2601	1	chr7B.!!$F1	634
16	TraesCS4A01G133600	chr6A	305186042	305186752	710	False	590.0	590	81.8690	1940	2647	1	chr6A.!!$F2	707
17	TraesCS4A01G133600	chr6A	367744945	367745456	511	True	363.0	363	80.0760	2137	2647	1	chr6A.!!$R2	510
18	TraesCS4A01G133600	chr7D	406001409	406002065	656	False	385.0	385	77.5940	1994	2647	1	chr7D.!!$F1	653

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
465	491	2.024176	ACACAAAGCAAGACACGACT	57.976	45.0	0.0	0.0	0.0	4.18	F
1240	2714	0.874390	GAAACCACGAGCAGCAATCA	59.126	50.0	0.0	0.0	0.0	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1528	3003	0.030235	CCCATACGTTCGAGATCGCA	59.97	55.0	0.0	0.0	39.6	5.10	R
2460	3957	0.600255	AAGAGCAACCAAGACCGACG	60.60	55.0	0.0	0.0	0.0	5.12	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
192	199	7.994334	TGATTACAGGTAAAGGTAACAACAGTT	59.006	33.333	0.00	0.00	41.41	3.16
238	250	5.104693	TCAGGATAGGATTAACGGAAAGCAA	60.105	40.000	0.00	0.00	0.00	3.91
379	403	3.490759	CACGGACATCGGCAGCAC	61.491	66.667	0.00	0.00	44.45	4.40
406	430	3.118847	GGGGTCTACCGGAAAGAAGTAAG	60.119	52.174	9.46	0.00	41.60	2.34
465	491	2.024176	ACACAAAGCAAGACACGACT	57.976	45.000	0.00	0.00	0.00	4.18
583	612	3.933048	GACGGACCAGAGGGGACGA	62.933	68.421	0.00	0.00	41.00	4.20
606	635	3.497332	TGTAGGTTCGCTATGCTAGGAT	58.503	45.455	1.17	1.17	0.00	3.24
625	654	3.656045	GTGTGGCGGACAAACGGG	61.656	66.667	0.00	0.00	35.91	5.28
650	679	4.789629	CACGTATTTGTATTCGTCTCGTCA	59.210	41.667	0.00	0.00	35.90	4.35
655	684	7.585210	CGTATTTGTATTCGTCTCGTCATTCTA	59.415	37.037	0.00	0.00	0.00	2.10
658	687	6.673154	TGTATTCGTCTCGTCATTCTAAGA	57.327	37.500	0.00	0.00	0.00	2.10
1159	2633	1.293498	CTACGCAAGGGACAGCAGT	59.707	57.895	0.00	0.00	46.39	4.40
1173	2647	2.182842	GCAGTAGGCGATTGCAGGG	61.183	63.158	10.07	0.00	45.35	4.45
1238	2712	1.577328	CGGAAACCACGAGCAGCAAT	61.577	55.000	0.00	0.00	0.00	3.56
1240	2714	0.874390	GAAACCACGAGCAGCAATCA	59.126	50.000	0.00	0.00	0.00	2.57
1254	2728	3.899981	AATCAGTTGCGGAGGCGCA	62.900	57.895	10.83	0.00	44.10	6.09
1364	2838	2.091640	TTGGGCTTCCTTCCATGGCA	62.092	55.000	6.96	0.00	32.48	4.92
1503	2978	1.819288	AGCGAACCGAAGAAGAGATGA	59.181	47.619	0.00	0.00	0.00	2.92
1527	3002	3.518998	CCGTGGCGAGGAGACGAT	61.519	66.667	0.00	0.00	35.05	3.73
1528	3003	2.490217	CGTGGCGAGGAGACGATT	59.510	61.111	0.00	0.00	35.05	3.34
1534	3009	1.272114	GCGAGGAGACGATTGCGATC	61.272	60.000	3.59	3.59	41.64	3.69
1554	3030	4.171103	GAACGTATGGGCCGCCCT	62.171	66.667	28.97	16.57	45.70	5.19
1576	3052	2.124320	CGATTTGGTGCCCGGGAT	60.124	61.111	29.31	7.39	0.00	3.85
1605	3081	3.075005	GCCACGCTGGACCTCCTA	61.075	66.667	8.04	0.00	40.96	2.94
1609	3085	0.681564	CACGCTGGACCTCCTAGACT	60.682	60.000	0.00	0.00	36.82	3.24
1630	3106	2.798364	TTCCCGAGTGCCAACGTCA	61.798	57.895	0.00	0.00	0.00	4.35
1877	3357	0.419459	ATGAAGGAGAGGGGAGGTGT	59.581	55.000	0.00	0.00	0.00	4.16
1951	3431	4.262036	CCCTTCTTACCTTCCTTTTTGTGC	60.262	45.833	0.00	0.00	0.00	4.57
2156	3638	2.003937	TTCCTAGGGGCAAACCAAAC	57.996	50.000	9.46	0.00	42.91	2.93
2210	3692	6.909550	TTACTTGGTGAATATTTGCAACCT	57.090	33.333	0.00	0.00	0.00	3.50
2363	3854	5.105917	TGTGATTACTGTAGATGAGCAACGA	60.106	40.000	0.00	0.00	0.00	3.85
2424	3915	5.360144	TCCCGAGATTTAAGAGGTAGAGTTG	59.640	44.000	0.00	0.00	0.00	3.16
2432	3929	3.562108	AGAGGTAGAGTTGAGGGGAAA	57.438	47.619	0.00	0.00	0.00	3.13
2435	3932	3.838903	GAGGTAGAGTTGAGGGGAAAGAA	59.161	47.826	0.00	0.00	0.00	2.52
2437	3934	4.471747	AGGTAGAGTTGAGGGGAAAGAATC	59.528	45.833	0.00	0.00	0.00	2.52
2439	3936	2.237392	AGAGTTGAGGGGAAAGAATCGG	59.763	50.000	0.00	0.00	0.00	4.18
2441	3938	2.375509	AGTTGAGGGGAAAGAATCGGTT	59.624	45.455	0.00	0.00	0.00	4.44
2443	3940	4.227527	AGTTGAGGGGAAAGAATCGGTTAT	59.772	41.667	0.00	0.00	0.00	1.89
2444	3941	4.150897	TGAGGGGAAAGAATCGGTTATG	57.849	45.455	0.00	0.00	0.00	1.90
2458	3955	7.435488	AGAATCGGTTATGAATTCTAACGAGTG	59.565	37.037	16.47	9.39	31.26	3.51
2460	3957	6.032094	TCGGTTATGAATTCTAACGAGTGTC	58.968	40.000	7.05	0.20	31.26	3.67
2481	3978	0.034896	TCGGTCTTGGTTGCTCTTCC	59.965	55.000	0.00	0.00	0.00	3.46
2488	3985	0.034896	TGGTTGCTCTTCCCGAAGAC	59.965	55.000	2.98	2.48	42.06	3.01
2496	3993	2.164624	CTCTTCCCGAAGACGTTGATCT	59.835	50.000	2.98	0.00	42.06	2.75
2522	4019	4.326826	TCGTTGATGCCTTCATTTCTCTT	58.673	39.130	0.00	0.00	33.34	2.85
2527	4024	4.946157	TGATGCCTTCATTTCTCTTCTTCC	59.054	41.667	0.00	0.00	31.96	3.46
2535	4032	2.941453	TTCTCTTCTTCCGGTCATCG	57.059	50.000	0.00	0.00	38.88	3.84
2578	4078	2.424956	GGGAACTCCATCGTACTTACGT	59.575	50.000	8.56	0.00	43.24	3.57
2583	4083	6.753744	GGAACTCCATCGTACTTACGTAAAAT	59.246	38.462	9.68	3.36	42.11	1.82
2584	4084	7.253883	GGAACTCCATCGTACTTACGTAAAATG	60.254	40.741	9.68	6.37	42.11	2.32
2608	4111	0.890683	GGGGTAACTCGAAGGAACGA	59.109	55.000	0.00	0.00	40.00	3.85
2610	4113	2.289010	GGGGTAACTCGAAGGAACGAAA	60.289	50.000	0.00	0.00	41.67	3.46
2615	4118	3.014604	ACTCGAAGGAACGAAACTCTG	57.985	47.619	0.00	0.00	41.67	3.35
2618	4121	2.069273	CGAAGGAACGAAACTCTGCAT	58.931	47.619	0.00	0.00	35.09	3.96
2620	4123	2.839486	AGGAACGAAACTCTGCATGA	57.161	45.000	0.00	0.00	0.00	3.07

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
2	3	1.926511	TAAAGTCGGGTCGGCTCGTC	61.927	60.000	10.08	2.91	42.48	4.20
171	176	5.503002	ACAACTGTTGTTACCTTTACCTGT	58.497	37.500	19.85	0.00	42.22	4.00
192	199	2.304470	TGCATAGCCTGTCCTTGTTACA	59.696	45.455	0.00	0.00	0.00	2.41
238	250	6.823182	TGCATTAGAGTTGTGTAGCATGTTAT	59.177	34.615	0.00	0.00	0.00	1.89
252	264	5.420421	TCTCTCTACTGCTTGCATTAGAGTT	59.580	40.000	30.79	4.93	39.02	3.01
406	430	2.911552	TTTATTGTGTTCCCCCTCCC	57.088	50.000	0.00	0.00	0.00	4.30
465	491	5.556006	GGTTACCCCTAGCACAACATATA	57.444	43.478	0.00	0.00	0.00	0.86
496	523	2.368875	CCTTTGCCGGTATCACCTATCT	59.631	50.000	1.90	0.00	35.66	1.98
583	612	3.895656	TCCTAGCATAGCGAACCTACAAT	59.104	43.478	0.00	0.00	37.37	2.71
625	654	3.061403	CGAGACGAATACAAATACGTGGC	60.061	47.826	0.00	0.00	39.04	5.01
750	780	5.733620	TGACTTAGTCAACCCGAATTAGT	57.266	39.130	13.16	0.00	39.78	2.24
1066	2517	0.807496	GCTCTTCTGTGTTGGATGCC	59.193	55.000	0.00	0.00	0.00	4.40
1159	2633	2.505982	GCTCCCTGCAATCGCCTA	59.494	61.111	0.00	0.00	42.31	3.93
1364	2838	3.422291	ACCCCCACCGTGTTTGGT	61.422	61.111	0.00	0.00	45.21	3.67
1527	3002	1.535226	CCCATACGTTCGAGATCGCAA	60.535	52.381	0.00	0.00	39.60	4.85
1528	3003	0.030235	CCCATACGTTCGAGATCGCA	59.970	55.000	0.00	0.00	39.60	5.10
1534	3009	2.960129	GCGGCCCATACGTTCGAG	60.960	66.667	0.00	0.00	0.00	4.04
1576	3052	4.351938	CGTGGCCGTCTTCGTCCA	62.352	66.667	0.00	0.00	42.87	4.02
1605	3081	1.371558	GGCACTCGGGAACAAGTCT	59.628	57.895	0.00	0.00	0.00	3.24
1609	3085	1.890041	CGTTGGCACTCGGGAACAA	60.890	57.895	0.00	0.00	0.00	2.83
1767	3243	0.485543	CCCCAAACCCCCTACAACTT	59.514	55.000	0.00	0.00	0.00	2.66
1842	3321	3.257873	CCTTCATCATCGCTACAGGAGAT	59.742	47.826	0.00	0.00	34.86	2.75
2156	3638	5.949354	TGTAGGAACCAACATTAAATGGAGG	59.051	40.000	11.11	2.62	39.12	4.30
2210	3692	6.795098	ACTGCAACACTAAAATGTTCGATA	57.205	33.333	0.00	0.00	40.89	2.92
2283	3769	3.328535	AAACCTCACTTGGGTCCAAAT	57.671	42.857	3.87	0.00	35.83	2.32
2363	3854	3.009143	GTGGAGGAGATTTGTAACACCCT	59.991	47.826	0.00	0.00	0.00	4.34
2424	3915	4.417426	TCATAACCGATTCTTTCCCCTC	57.583	45.455	0.00	0.00	0.00	4.30
2432	3929	7.435488	CACTCGTTAGAATTCATAACCGATTCT	59.565	37.037	8.44	0.00	35.90	2.40
2435	3932	6.570692	ACACTCGTTAGAATTCATAACCGAT	58.429	36.000	8.44	0.00	30.84	4.18
2437	3934	5.052567	CGACACTCGTTAGAATTCATAACCG	60.053	44.000	8.44	9.54	34.72	4.44
2458	3955	1.282930	GAGCAACCAAGACCGACGAC	61.283	60.000	0.00	0.00	0.00	4.34
2460	3957	0.600255	AAGAGCAACCAAGACCGACG	60.600	55.000	0.00	0.00	0.00	5.12
2481	3978	2.594654	CGAAAGAGATCAACGTCTTCGG	59.405	50.000	0.00	0.00	41.85	4.30
2488	3985	3.484229	GGCATCAACGAAAGAGATCAACG	60.484	47.826	0.00	0.00	0.00	4.10
2496	3993	4.761739	AGAAATGAAGGCATCAACGAAAGA	59.238	37.500	0.00	0.00	42.54	2.52
2522	4019	1.201647	GACTTCACGATGACCGGAAGA	59.798	52.381	9.46	0.00	42.66	2.87
2527	4024	1.778334	TGTTGACTTCACGATGACCG	58.222	50.000	0.00	0.00	45.44	4.79
2535	4032	4.083802	CCGAAGAAAGGATGTTGACTTCAC	60.084	45.833	0.00	0.00	35.11	3.18
2578	4078	7.126115	TCCTTCGAGTTACCCCTTATCATTTTA	59.874	37.037	0.00	0.00	0.00	1.52
2583	4083	3.985127	TCCTTCGAGTTACCCCTTATCA	58.015	45.455	0.00	0.00	0.00	2.15
2584	4084	4.691175	GTTCCTTCGAGTTACCCCTTATC	58.309	47.826	0.00	0.00	0.00	1.75
2585	4085	3.131755	CGTTCCTTCGAGTTACCCCTTAT	59.868	47.826	0.00	0.00	0.00	1.73
2602	4105	3.751621	CAATCATGCAGAGTTTCGTTCC	58.248	45.455	0.00	0.00	0.00	3.62
2618	4121	5.979993	TGTTATCTACCGGTTAAGCAATCA	58.020	37.500	15.04	0.42	0.00	2.57
2620	4123	7.660208	CCTAATGTTATCTACCGGTTAAGCAAT	59.340	37.037	15.04	0.00	0.00	3.56

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.