AutoCloner

Multiple sequence alignment - TraesCS4B01G030700

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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	TraesCS4B01G030700	chr4B	100.000	6374	0	0	1	6374	22899268	22892895	0.000000e+00	11771.0
1	TraesCS4B01G030700	chr4B	93.466	1913	94	17	3844	5744	22885812	22883919	0.000000e+00	2811.0
2	TraesCS4B01G030700	chr4B	89.044	429	30	6	5740	6153	22881792	22881366	3.410000e-142	516.0
3	TraesCS4B01G030700	chr4B	83.367	493	61	15	3943	4423	8412923	8412440	2.730000e-118	436.0
4	TraesCS4B01G030700	chr4B	95.294	255	12	0	2550	2804	126596124	126595870	7.690000e-109	405.0
5	TraesCS4B01G030700	chr4B	90.037	271	26	1	3579	3849	22886166	22885897	3.660000e-92	350.0
6	TraesCS4B01G030700	chr4B	89.855	276	20	3	2806	3075	22886431	22886158	1.320000e-91	348.0
7	TraesCS4B01G030700	chr4B	79.826	461	78	15	4600	5054	21395930	21396381	7.970000e-84	322.0
8	TraesCS4B01G030700	chr4B	93.889	180	6	2	6193	6372	22881364	22881190	3.790000e-67	267.0
9	TraesCS4B01G030700	chr4D	91.628	2341	145	17	3844	6153	12532316	12529996	0.000000e+00	3190.0
10	TraesCS4B01G030700	chr4D	94.301	1825	94	7	224	2043	12535070	12533251	0.000000e+00	2785.0
11	TraesCS4B01G030700	chr4D	94.472	1393	66	9	649	2038	12543253	12541869	0.000000e+00	2135.0
12	TraesCS4B01G030700	chr4D	94.033	1106	34	10	4331	5431	12539871	12538793	0.000000e+00	1648.0
13	TraesCS4B01G030700	chr4D	96.300	946	29	3	5429	6374	12538764	12537825	0.000000e+00	1548.0
14	TraesCS4B01G030700	chr4D	89.577	1065	63	17	2806	3853	12541544	12540511	0.000000e+00	1308.0
15	TraesCS4B01G030700	chr4D	95.622	434	14	2	224	653	12543785	12543353	0.000000e+00	691.0
16	TraesCS4B01G030700	chr4D	92.744	317	22	1	2233	2548	12533265	12532949	2.090000e-124	457.0
17	TraesCS4B01G030700	chr4D	93.204	309	20	1	2241	2548	12541866	12541558	2.710000e-123	453.0
18	TraesCS4B01G030700	chr4D	92.727	275	19	1	3579	3853	12532670	12532397	4.630000e-106	396.0
19	TraesCS4B01G030700	chr4D	90.580	276	18	3	2806	3075	12532935	12532662	6.080000e-95	359.0
20	TraesCS4B01G030700	chr4D	93.407	182	5	3	6191	6372	12529996	12529822	4.900000e-66	263.0
21	TraesCS4B01G030700	chr4A	93.818	1828	97	7	223	2044	590092188	590094005	0.000000e+00	2736.0
22	TraesCS4B01G030700	chr4A	92.576	1751	94	15	4432	6156	590097313	590099053	0.000000e+00	2481.0
23	TraesCS4B01G030700	chr4A	89.513	1068	80	15	2806	3850	590094319	590095377	0.000000e+00	1323.0
24	TraesCS4B01G030700	chr4A	88.833	600	64	3	3840	4437	590095457	590096055	0.000000e+00	734.0
25	TraesCS4B01G030700	chr4A	90.221	317	29	2	2233	2548	590093990	590094305	4.600000e-111	412.0
26	TraesCS4B01G030700	chr4A	95.055	182	7	1	6191	6372	590099049	590099228	1.050000e-72	285.0
27	TraesCS4B01G030700	chr4A	94.595	148	8	0	81	228	428284139	428284286	4.970000e-56	230.0
28	TraesCS4B01G030700	chrUn	93.538	1826	105	9	224	2043	357650771	357652589	0.000000e+00	2706.0
29	TraesCS4B01G030700	chr7D	85.842	558	50	16	3885	4424	543336337	543335791	3.340000e-157	566.0
30	TraesCS4B01G030700	chr7D	90.732	410	35	2	3428	3836	543352434	543352027	1.560000e-150	544.0
31	TraesCS4B01G030700	chr3A	88.967	426	41	4	3430	3853	608745475	608745054	7.320000e-144	521.0
32	TraesCS4B01G030700	chr3A	98.837	258	3	0	2547	2804	512035498	512035755	1.620000e-125	460.0
33	TraesCS4B01G030700	chr3A	85.176	398	41	7	4060	4441	79392698	79393093	5.990000e-105	392.0
34	TraesCS4B01G030700	chr7A	89.512	410	38	3	3428	3836	625369947	625369542	1.230000e-141	514.0
35	TraesCS4B01G030700	chr7A	97.255	255	7	0	2550	2804	365105293	365105039	3.530000e-117	433.0
36	TraesCS4B01G030700	chr7A	96.512	258	9	0	2547	2804	512766573	512766830	1.640000e-115	427.0
37	TraesCS4B01G030700	chr7A	91.018	167	15	0	59	225	158664920	158665086	6.430000e-55	226.0
38	TraesCS4B01G030700	chr2A	86.374	433	38	11	3429	3853	4352829	4352410	2.710000e-123	453.0
39	TraesCS4B01G030700	chr2A	94.595	148	8	0	81	228	469790056	469790203	4.970000e-56	230.0
40	TraesCS4B01G030700	chr2A	87.387	111	11	1	3037	3144	3517604	3517714	2.410000e-24	124.0
41	TraesCS4B01G030700	chr5B	97.674	258	6	0	2547	2804	385190127	385190384	1.630000e-120	444.0
42	TraesCS4B01G030700	chr5B	87.896	347	36	5	4080	4423	110129314	110128971	2.770000e-108	403.0
43	TraesCS4B01G030700	chr5B	85.765	281	22	5	3573	3853	507761615	507761353	1.350000e-71	281.0
44	TraesCS4B01G030700	chr5B	90.751	173	14	1	53	225	648279369	648279539	4.970000e-56	230.0
45	TraesCS4B01G030700	chr5B	91.463	164	14	0	62	225	594099162	594098999	6.430000e-55	226.0
46	TraesCS4B01G030700	chr1B	88.347	369	35	7	4060	4424	630752839	630752475	2.730000e-118	436.0
47	TraesCS4B01G030700	chr1B	89.109	303	28	5	4124	4423	45818230	45817930	7.800000e-99	372.0
48	TraesCS4B01G030700	chr1B	84.000	125	16	2	3031	3151	3239963	3240087	4.040000e-22	117.0
49	TraesCS4B01G030700	chr6B	96.863	255	8	0	2550	2804	125640391	125640137	1.640000e-115	427.0
50	TraesCS4B01G030700	chr6B	95.294	255	12	0	2550	2804	442430141	442429887	7.690000e-109	405.0
51	TraesCS4B01G030700	chr7B	96.047	253	10	0	2552	2804	72765102	72765354	4.600000e-111	412.0
52	TraesCS4B01G030700	chr2B	95.057	263	8	1	2547	2804	440825753	440826015	5.950000e-110	409.0
53	TraesCS4B01G030700	chr2B	86.400	125	14	1	3031	3152	212020012	212019888	4.010000e-27	134.0
54	TraesCS4B01G030700	chr2B	85.000	120	15	1	3035	3151	210463907	210463788	1.120000e-22	119.0
55	TraesCS4B01G030700	chr3B	93.158	190	12	1	2046	2234	600911692	600911503	1.750000e-70	278.0
56	TraesCS4B01G030700	chr3B	97.059	34	1	0	2126	2159	104332984	104333017	2.480000e-04	58.4
57	TraesCS4B01G030700	chr1D	95.833	144	6	0	82	225	327856852	327856995	3.840000e-57	233.0
58	TraesCS4B01G030700	chr5D	90.909	165	14	1	63	226	135238512	135238676	2.990000e-53	220.0
59	TraesCS4B01G030700	chr5D	86.066	122	13	2	3033	3151	482404582	482404462	1.870000e-25	128.0
60	TraesCS4B01G030700	chr5D	85.484	124	15	1	3040	3160	444300468	444300345	6.710000e-25	126.0
61	TraesCS4B01G030700	chr5D	84.252	127	15	2	3034	3155	361510358	361510232	1.120000e-22	119.0
62	TraesCS4B01G030700	chr6D	89.266	177	15	4	59	235	41542508	41542336	1.080000e-52	219.0
63	TraesCS4B01G030700	chr3D	92.667	150	11	0	3704	3853	443423681	443423830	3.870000e-52	217.0
64	TraesCS4B01G030700	chr5A	87.568	185	19	3	53	235	623008706	623008888	1.800000e-50	211.0

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	TraesCS4B01G030700	chr4B	22892895	22899268	6373	True	11771.000000	11771	100.000000	1	6374	1	chr4B.!!$R2	6373
1	TraesCS4B01G030700	chr4B	22881190	22886431	5241	True	858.400000	2811	91.258200	2806	6372	5	chr4B.!!$R4	3566
2	TraesCS4B01G030700	chr4D	12529822	12543785	13963	True	1269.416667	3190	93.216250	224	6374	12	chr4D.!!$R1	6150
3	TraesCS4B01G030700	chr4A	590092188	590099228	7040	False	1328.500000	2736	91.669333	223	6372	6	chr4A.!!$F2	6149
4	TraesCS4B01G030700	chrUn	357650771	357652589	1818	False	2706.000000	2706	93.538000	224	2043	1	chrUn.!!$F1	1819
5	TraesCS4B01G030700	chr7D	543335791	543336337	546	True	566.000000	566	85.842000	3885	4424	1	chr7D.!!$R1	539

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
44	45	0.096976	GCGTTTCGATGGTGGTGATG	59.903	55.000	0.00	0.0	0.00	3.07	F
84	85	0.178998	TCGGACGGAGGGAGGATAAG	60.179	60.000	0.00	0.0	0.00	1.73	F
85	86	0.467659	CGGACGGAGGGAGGATAAGT	60.468	60.000	0.00	0.0	0.00	2.24	F
87	88	1.133419	GGACGGAGGGAGGATAAGTCT	60.133	57.143	0.00	0.0	0.00	3.24	F
1731	1842	1.379044	CCGAATTGCAGGGGAGCTT	60.379	57.895	0.00	0.0	34.99	3.74	F
2153	2266	0.108138	GTGGGAGTCCGATGTTCCAG	60.108	60.000	2.26	0.0	35.24	3.86	F
2736	2850	0.037590	TGTAGCGGGCAGTGGAAAAT	59.962	50.000	0.00	0.0	0.00	1.82	F
2738	2852	0.326595	TAGCGGGCAGTGGAAAATCA	59.673	50.000	0.00	0.0	0.00	2.57	F
3047	3167	0.332632	CCTCCAAAATGCTCCCTCCA	59.667	55.000	0.00	0.0	0.00	3.86	F
4553	14265	0.394938	TTGTGGTGCGTGGATACTGT	59.605	50.000	0.00	0.0	37.61	3.55	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1731	1842	0.895100	GTGCCACCTTCAGCAATGGA	60.895	55.000	0.00	0.00	41.48	3.41	R
2051	2164	0.591170	GCACTGCGCCTACAAAAAGA	59.409	50.000	4.18	0.00	32.94	2.52	R
2062	2175	1.270971	CAACATTATTGGCACTGCGC	58.729	50.000	0.00	0.00	41.28	6.09	R
2064	2177	2.367030	TGCAACATTATTGGCACTGC	57.633	45.000	0.00	0.00	0.00	4.40	R
2717	2831	0.037590	ATTTTCCACTGCCCGCTACA	59.962	50.000	0.00	0.00	0.00	2.74	R
3161	3281	0.257039	AGGGTCATGGAATGCACTCC	59.743	55.000	7.40	7.40	46.21	3.85	R
3576	3720	0.461339	CAACCGGGTCCCACTTATCG	60.461	60.000	9.12	0.00	0.00	2.92	R
4098	4443	1.621822	ACGGACTCCCTCCTCCCTA	60.622	63.158	0.00	0.00	36.80	3.53	R
4802	14518	1.354368	TCCTTTCCAGCGGATTTTCCT	59.646	47.619	0.00	0.00	33.30	3.36	R
6159	18031	0.187117	TTGAAAGTGGCCACCCATGA	59.813	50.000	32.29	13.29	44.51	3.07	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)

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
20	21	3.439857	TCTTGACTTTGCTATTGCCCT	57.560	42.857	0.00	0.00	38.71	5.19
21	22	3.084039	TCTTGACTTTGCTATTGCCCTG	58.916	45.455	0.00	0.00	38.71	4.45
22	23	2.877097	TGACTTTGCTATTGCCCTGA	57.123	45.000	0.00	0.00	38.71	3.86
23	24	3.370840	TGACTTTGCTATTGCCCTGAT	57.629	42.857	0.00	0.00	38.71	2.90
24	25	3.018856	TGACTTTGCTATTGCCCTGATG	58.981	45.455	0.00	0.00	38.71	3.07
25	26	2.360165	GACTTTGCTATTGCCCTGATGG	59.640	50.000	0.00	0.00	38.71	3.51
34	35	4.540153	CCCTGATGGCGTTTCGAT	57.460	55.556	0.00	0.00	0.00	3.59
35	36	2.016961	CCCTGATGGCGTTTCGATG	58.983	57.895	0.00	0.00	0.00	3.84
36	37	1.439353	CCCTGATGGCGTTTCGATGG	61.439	60.000	0.00	0.00	0.00	3.51
37	38	0.744414	CCTGATGGCGTTTCGATGGT	60.744	55.000	0.00	0.00	0.00	3.55
38	39	0.374758	CTGATGGCGTTTCGATGGTG	59.625	55.000	0.00	0.00	0.00	4.17
39	40	1.024046	TGATGGCGTTTCGATGGTGG	61.024	55.000	0.00	0.00	0.00	4.61
40	41	1.002624	ATGGCGTTTCGATGGTGGT	60.003	52.632	0.00	0.00	0.00	4.16
41	42	1.305219	ATGGCGTTTCGATGGTGGTG	61.305	55.000	0.00	0.00	0.00	4.17
42	43	1.669760	GGCGTTTCGATGGTGGTGA	60.670	57.895	0.00	0.00	0.00	4.02
43	44	1.024579	GGCGTTTCGATGGTGGTGAT	61.025	55.000	0.00	0.00	0.00	3.06
44	45	0.096976	GCGTTTCGATGGTGGTGATG	59.903	55.000	0.00	0.00	0.00	3.07
45	46	1.720805	CGTTTCGATGGTGGTGATGA	58.279	50.000	0.00	0.00	0.00	2.92
46	47	1.660607	CGTTTCGATGGTGGTGATGAG	59.339	52.381	0.00	0.00	0.00	2.90
47	48	2.009774	GTTTCGATGGTGGTGATGAGG	58.990	52.381	0.00	0.00	0.00	3.86
48	49	1.275666	TTCGATGGTGGTGATGAGGT	58.724	50.000	0.00	0.00	0.00	3.85
49	50	1.275666	TCGATGGTGGTGATGAGGTT	58.724	50.000	0.00	0.00	0.00	3.50
50	51	2.462723	TCGATGGTGGTGATGAGGTTA	58.537	47.619	0.00	0.00	0.00	2.85
51	52	3.038280	TCGATGGTGGTGATGAGGTTAT	58.962	45.455	0.00	0.00	0.00	1.89
52	53	3.133691	CGATGGTGGTGATGAGGTTATG	58.866	50.000	0.00	0.00	0.00	1.90

Showing 1 to 25 of 504 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
0	1	3.084039	CAGGGCAATAGCAAAGTCAAGA	58.916	45.455	0.00	0.00	44.61	3.02
1	2	3.084039	TCAGGGCAATAGCAAAGTCAAG	58.916	45.455	0.00	0.00	44.61	3.02
2	3	3.153369	TCAGGGCAATAGCAAAGTCAA	57.847	42.857	0.00	0.00	44.61	3.18
3	4	2.877097	TCAGGGCAATAGCAAAGTCA	57.123	45.000	0.00	0.00	44.61	3.41
4	5	2.360165	CCATCAGGGCAATAGCAAAGTC	59.640	50.000	0.00	0.00	44.61	3.01
5	6	2.381911	CCATCAGGGCAATAGCAAAGT	58.618	47.619	0.00	0.00	44.61	2.66
17	18	1.439353	CCATCGAAACGCCATCAGGG	61.439	60.000	0.00	0.00	40.85	4.45
18	19	0.744414	ACCATCGAAACGCCATCAGG	60.744	55.000	0.00	0.00	38.23	3.86
19	20	0.374758	CACCATCGAAACGCCATCAG	59.625	55.000	0.00	0.00	0.00	2.90
20	21	1.024046	CCACCATCGAAACGCCATCA	61.024	55.000	0.00	0.00	0.00	3.07
21	22	1.024579	ACCACCATCGAAACGCCATC	61.025	55.000	0.00	0.00	0.00	3.51
22	23	1.002624	ACCACCATCGAAACGCCAT	60.003	52.632	0.00	0.00	0.00	4.40
23	24	1.963855	CACCACCATCGAAACGCCA	60.964	57.895	0.00	0.00	0.00	5.69
24	25	1.024579	ATCACCACCATCGAAACGCC	61.025	55.000	0.00	0.00	0.00	5.68
25	26	0.096976	CATCACCACCATCGAAACGC	59.903	55.000	0.00	0.00	0.00	4.84
26	27	1.660607	CTCATCACCACCATCGAAACG	59.339	52.381	0.00	0.00	0.00	3.60
27	28	2.009774	CCTCATCACCACCATCGAAAC	58.990	52.381	0.00	0.00	0.00	2.78
28	29	1.628340	ACCTCATCACCACCATCGAAA	59.372	47.619	0.00	0.00	0.00	3.46
29	30	1.275666	ACCTCATCACCACCATCGAA	58.724	50.000	0.00	0.00	0.00	3.71
30	31	1.275666	AACCTCATCACCACCATCGA	58.724	50.000	0.00	0.00	0.00	3.59
31	32	2.979814	TAACCTCATCACCACCATCG	57.020	50.000	0.00	0.00	0.00	3.84
32	33	4.130118	GACATAACCTCATCACCACCATC	58.870	47.826	0.00	0.00	0.00	3.51
33	34	3.523157	TGACATAACCTCATCACCACCAT	59.477	43.478	0.00	0.00	0.00	3.55
34	35	2.909662	TGACATAACCTCATCACCACCA	59.090	45.455	0.00	0.00	0.00	4.17
35	36	3.627395	TGACATAACCTCATCACCACC	57.373	47.619	0.00	0.00	0.00	4.61

Showing 1 to 25 of 568 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.