AutoCloner

Multiple sequence alignment - TraesCS6D01G232900

Loading Multiple Alignment...

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	TraesCS6D01G232900	chr6D	100.000	1568	0	0	718	2285	327001640	327000073	0.000000e+00	2896.0
1	TraesCS6D01G232900	chr6D	100.000	583	0	0	1	583	327002357	327001775	0.000000e+00	1077.0
2	TraesCS6D01G232900	chr6D	94.541	458	19	6	128	583	8984499	8984046	0.000000e+00	702.0
3	TraesCS6D01G232900	chr3D	97.559	1475	35	1	718	2191	571521955	571520481	0.000000e+00	2523.0
4	TraesCS6D01G232900	chr3D	96.084	1481	51	4	718	2191	2390698	2392178	0.000000e+00	2407.0
5	TraesCS6D01G232900	chr3D	96.016	1481	53	4	718	2196	55541475	55542951	0.000000e+00	2403.0
6	TraesCS6D01G232900	chr3D	94.785	441	21	2	144	583	15846032	15846471	0.000000e+00	686.0
7	TraesCS6D01G232900	chr3D	94.395	446	21	4	140	583	331073876	331073433	0.000000e+00	682.0
8	TraesCS6D01G232900	chr5D	97.017	1475	43	1	718	2191	371076610	371075136	0.000000e+00	2479.0
9	TraesCS6D01G232900	chr5D	96.746	1475	46	2	718	2191	193611336	193609863	0.000000e+00	2457.0
10	TraesCS6D01G232900	chr5D	95.932	1475	54	5	718	2191	417810571	417812040	0.000000e+00	2386.0
11	TraesCS6D01G232900	chr5D	96.214	449	15	2	136	583	26843758	26843311	0.000000e+00	734.0
12	TraesCS6D01G232900	chr5D	95.730	445	15	3	143	583	77888797	77888353	0.000000e+00	713.0
13	TraesCS6D01G232900	chr5D	93.913	115	4	3	2171	2285	489609844	489609733	1.090000e-38	171.0
14	TraesCS6D01G232900	chr1D	96.339	1475	51	2	718	2191	443108544	443110016	0.000000e+00	2422.0
15	TraesCS6D01G232900	chr1D	96.372	441	15	1	144	583	114304469	114304909	0.000000e+00	725.0
16	TraesCS6D01G232900	chr1D	98.000	100	2	0	2186	2285	339090274	339090175	8.390000e-40	174.0
17	TraesCS6D01G232900	chr1D	96.190	105	2	2	2182	2285	221302246	221302349	1.090000e-38	171.0
18	TraesCS6D01G232900	chr7D	95.932	1475	58	2	718	2191	501413647	501412174	0.000000e+00	2390.0
19	TraesCS6D01G232900	chr7D	94.222	450	22	3	136	583	102554032	102554479	0.000000e+00	684.0
20	TraesCS6D01G232900	chr7D	95.327	107	4	1	2180	2285	565517932	565518038	3.900000e-38	169.0
21	TraesCS6D01G232900	chr7D	94.521	73	4	0	1	73	575081261	575081189	1.860000e-21	113.0
22	TraesCS6D01G232900	chr4D	94.915	1475	72	3	718	2191	98461626	98460154	0.000000e+00	2305.0
23	TraesCS6D01G232900	chr4D	94.796	442	19	4	144	583	85734579	85735018	0.000000e+00	686.0
24	TraesCS6D01G232900	chr7A	94.369	444	21	4	143	583	699472764	699472322	0.000000e+00	678.0
25	TraesCS6D01G232900	chr1A	95.327	107	4	1	2180	2285	509007958	509007852	3.900000e-38	169.0
26	TraesCS6D01G232900	chr7B	93.043	115	3	4	2174	2285	703253274	703253386	1.820000e-36	163.0
27	TraesCS6D01G232900	chr7B	94.340	106	5	1	2180	2285	604355202	604355098	6.530000e-36	161.0
28	TraesCS6D01G232900	chr7B	90.756	119	7	3	2170	2285	259966247	259966130	3.040000e-34	156.0
29	TraesCS6D01G232900	chr4B	97.872	94	2	0	2192	2285	30030316	30030223	1.820000e-36	163.0
30	TraesCS6D01G232900	chr4B	93.243	74	5	0	1	74	647711279	647711352	2.400000e-20	110.0
31	TraesCS6D01G232900	chr4B	94.828	58	3	0	4	61	648094504	648094447	8.690000e-15	91.6
32	TraesCS6D01G232900	chr2A	94.444	72	4	0	3	74	85293427	85293498	6.670000e-21	111.0
33	TraesCS6D01G232900	chr5A	95.082	61	3	0	3	63	589583610	589583670	1.870000e-16	97.1
34	TraesCS6D01G232900	chr5A	93.220	59	4	0	3	61	92220206	92220148	1.120000e-13	87.9
35	TraesCS6D01G232900	chr2B	96.875	32	1	0	39	70	23918126	23918095	1.000000e-03	54.7

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	TraesCS6D01G232900	chr6D	327000073	327002357	2284	True	1986.5	2896	100.000	1	2285	2	chr6D.!!$R2	2284
1	TraesCS6D01G232900	chr3D	571520481	571521955	1474	True	2523.0	2523	97.559	718	2191	1	chr3D.!!$R2	1473
2	TraesCS6D01G232900	chr3D	2390698	2392178	1480	False	2407.0	2407	96.084	718	2191	1	chr3D.!!$F1	1473
3	TraesCS6D01G232900	chr3D	55541475	55542951	1476	False	2403.0	2403	96.016	718	2196	1	chr3D.!!$F3	1478
4	TraesCS6D01G232900	chr5D	371075136	371076610	1474	True	2479.0	2479	97.017	718	2191	1	chr5D.!!$R4	1473
5	TraesCS6D01G232900	chr5D	193609863	193611336	1473	True	2457.0	2457	96.746	718	2191	1	chr5D.!!$R3	1473
6	TraesCS6D01G232900	chr5D	417810571	417812040	1469	False	2386.0	2386	95.932	718	2191	1	chr5D.!!$F1	1473
7	TraesCS6D01G232900	chr1D	443108544	443110016	1472	False	2422.0	2422	96.339	718	2191	1	chr1D.!!$F3	1473
8	TraesCS6D01G232900	chr7D	501412174	501413647	1473	True	2390.0	2390	95.932	718	2191	1	chr7D.!!$R1	1473
9	TraesCS6D01G232900	chr4D	98460154	98461626	1472	True	2305.0	2305	94.915	718	2191	1	chr4D.!!$R1	1473

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
390	391	0.034198	TGTGTAAAGTGCAGCGCCTA	59.966	50.0	2.29	0.0	0.0	3.93	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
1448	1451	0.605589	TCTGACGACGCTCTTCCTCA	60.606	55.0	0.0	0.0	0.0	3.86	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
23	24	6.566197	GCCTTAATCATATGGAAGTGAAGG	57.434	41.667	2.13	8.63	0.00	3.46
24	25	6.299141	GCCTTAATCATATGGAAGTGAAGGA	58.701	40.000	16.87	0.00	0.00	3.36
25	26	6.429385	GCCTTAATCATATGGAAGTGAAGGAG	59.571	42.308	16.87	3.34	0.00	3.69
26	27	6.939163	CCTTAATCATATGGAAGTGAAGGAGG	59.061	42.308	2.13	0.00	0.00	4.30
27	28	4.989875	ATCATATGGAAGTGAAGGAGGG	57.010	45.455	2.13	0.00	0.00	4.30
28	29	4.007581	TCATATGGAAGTGAAGGAGGGA	57.992	45.455	2.13	0.00	0.00	4.20
29	30	4.370776	TCATATGGAAGTGAAGGAGGGAA	58.629	43.478	2.13	0.00	0.00	3.97
30	31	4.410228	TCATATGGAAGTGAAGGAGGGAAG	59.590	45.833	2.13	0.00	0.00	3.46
31	32	2.118403	TGGAAGTGAAGGAGGGAAGT	57.882	50.000	0.00	0.00	0.00	3.01
32	33	2.418669	TGGAAGTGAAGGAGGGAAGTT	58.581	47.619	0.00	0.00	0.00	2.66
33	34	3.593942	TGGAAGTGAAGGAGGGAAGTTA	58.406	45.455	0.00	0.00	0.00	2.24
34	35	3.583086	TGGAAGTGAAGGAGGGAAGTTAG	59.417	47.826	0.00	0.00	0.00	2.34
35	36	3.055021	GGAAGTGAAGGAGGGAAGTTAGG	60.055	52.174	0.00	0.00	0.00	2.69
36	37	2.552367	AGTGAAGGAGGGAAGTTAGGG	58.448	52.381	0.00	0.00	0.00	3.53
37	38	2.113777	AGTGAAGGAGGGAAGTTAGGGA	59.886	50.000	0.00	0.00	0.00	4.20
38	39	2.910977	GTGAAGGAGGGAAGTTAGGGAA	59.089	50.000	0.00	0.00	0.00	3.97
39	40	3.055021	GTGAAGGAGGGAAGTTAGGGAAG	60.055	52.174	0.00	0.00	0.00	3.46
40	41	3.182976	GAAGGAGGGAAGTTAGGGAAGT	58.817	50.000	0.00	0.00	0.00	3.01
41	42	2.552367	AGGAGGGAAGTTAGGGAAGTG	58.448	52.381	0.00	0.00	0.00	3.16
42	43	2.157989	AGGAGGGAAGTTAGGGAAGTGT	60.158	50.000	0.00	0.00	0.00	3.55
43	44	3.078612	AGGAGGGAAGTTAGGGAAGTGTA	59.921	47.826	0.00	0.00	0.00	2.90
44	45	3.451540	GGAGGGAAGTTAGGGAAGTGTAG	59.548	52.174	0.00	0.00	0.00	2.74
45	46	2.838813	AGGGAAGTTAGGGAAGTGTAGC	59.161	50.000	0.00	0.00	0.00	3.58
46	47	2.838813	GGGAAGTTAGGGAAGTGTAGCT	59.161	50.000	0.00	0.00	0.00	3.32
47	48	3.263681	GGGAAGTTAGGGAAGTGTAGCTT	59.736	47.826	0.00	0.00	40.76	3.74

Showing 1 to 25 of 384 entries

Previous1 2 3 4 5…16Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	End Stability
0	1	6.299141	TCCTTCACTTCCATATGATTAAGGC	58.701	40.000	3.65	0.00	4.35
1	2	6.939163	CCTCCTTCACTTCCATATGATTAAGG	59.061	42.308	3.65	8.25	2.69
2	3	6.939163	CCCTCCTTCACTTCCATATGATTAAG	59.061	42.308	3.65	7.48	1.85
3	4	6.619437	TCCCTCCTTCACTTCCATATGATTAA	59.381	38.462	3.65	0.00	1.40
4	5	6.150332	TCCCTCCTTCACTTCCATATGATTA	58.850	40.000	3.65	0.00	1.75
5	6	4.977739	TCCCTCCTTCACTTCCATATGATT	59.022	41.667	3.65	0.00	2.57
6	7	4.570926	TCCCTCCTTCACTTCCATATGAT	58.429	43.478	3.65	0.00	2.45
7	8	4.007581	TCCCTCCTTCACTTCCATATGA	57.992	45.455	3.65	0.00	2.15
8	9	4.164988	ACTTCCCTCCTTCACTTCCATATG	59.835	45.833	0.00	0.00	1.78
9	10	4.375313	ACTTCCCTCCTTCACTTCCATAT	58.625	43.478	0.00	0.00	1.78
10	11	3.803340	ACTTCCCTCCTTCACTTCCATA	58.197	45.455	0.00	0.00	2.74
11	12	2.637165	ACTTCCCTCCTTCACTTCCAT	58.363	47.619	0.00	0.00	3.41
12	13	2.118403	ACTTCCCTCCTTCACTTCCA	57.882	50.000	0.00	0.00	3.53
13	14	3.055021	CCTAACTTCCCTCCTTCACTTCC	60.055	52.174	0.00	0.00	3.46
14	15	3.055021	CCCTAACTTCCCTCCTTCACTTC	60.055	52.174	0.00	0.00	3.01
15	16	2.913617	CCCTAACTTCCCTCCTTCACTT	59.086	50.000	0.00	0.00	3.16
16	17	2.113777	TCCCTAACTTCCCTCCTTCACT	59.886	50.000	0.00	0.00	3.41
17	18	2.547990	TCCCTAACTTCCCTCCTTCAC	58.452	52.381	0.00	0.00	3.18
18	19	3.182152	CTTCCCTAACTTCCCTCCTTCA	58.818	50.000	0.00	0.00	3.02
19	20	3.055021	CACTTCCCTAACTTCCCTCCTTC	60.055	52.174	0.00	0.00	3.46
20	21	2.913617	CACTTCCCTAACTTCCCTCCTT	59.086	50.000	0.00	0.00	3.36
21	22	2.157989	ACACTTCCCTAACTTCCCTCCT	60.158	50.000	0.00	0.00	3.69
22	23	2.267192	ACACTTCCCTAACTTCCCTCC	58.733	52.381	0.00	0.00	4.30
23	24	3.118702	GCTACACTTCCCTAACTTCCCTC	60.119	52.174	0.00	0.00	4.30
24	25	2.838813	GCTACACTTCCCTAACTTCCCT	59.161	50.000	0.00	0.00	4.20

Showing 1 to 25 of 387 entries

Previous1 2 3 4 5…16Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.