AutoCloner

Multiple sequence alignment - TraesCS5B01G508500

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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	TraesCS5B01G508500	chr5B	100.000	2959	0	0	944	3902	673679865	673682823	0.000000e+00	5465.0
1	TraesCS5B01G508500	chr5B	100.000	648	0	0	1	648	673678922	673679569	0.000000e+00	1197.0
2	TraesCS5B01G508500	chr5B	81.126	604	54	16	944	1543	673636177	673636724	2.790000e-116	429.0
3	TraesCS5B01G508500	chr5B	85.498	331	36	7	944	1274	673670126	673670444	6.250000e-88	335.0
4	TraesCS5B01G508500	chr5B	89.510	143	13	2	1275	1417	673670682	673670822	3.100000e-41	180.0
5	TraesCS5B01G508500	chr5B	86.275	102	6	3	1827	1921	673638691	673638791	1.920000e-18	104.0
6	TraesCS5B01G508500	chr5B	91.667	72	4	2	1446	1517	673671539	673671608	8.920000e-17	99.0
7	TraesCS5B01G508500	chr5B	85.870	92	10	3	3247	3336	568731929	568732019	1.150000e-15	95.3
8	TraesCS5B01G508500	chr5D	89.638	2210	145	37	1602	3779	533631269	533633426	0.000000e+00	2736.0
9	TraesCS5B01G508500	chr5D	90.772	531	23	8	1021	1543	533630701	533631213	0.000000e+00	686.0
10	TraesCS5B01G508500	chr5D	82.011	378	34	17	1131	1506	533576168	533576513	1.370000e-74	291.0
11	TraesCS5B01G508500	chr5D	85.965	114	10	2	535	642	533629834	533629947	2.460000e-22	117.0
12	TraesCS5B01G508500	chr5D	95.455	44	2	0	1290	1333	533545493	533545536	1.950000e-08	71.3
13	TraesCS5B01G508500	chr5D	100.000	29	0	0	1572	1600	533631215	533631243	2.000000e-03	54.7
14	TraesCS5B01G508500	chr4A	86.177	1823	125	69	1600	3366	638221797	638220046	0.000000e+00	1853.0
15	TraesCS5B01G508500	chr4A	88.816	608	39	16	947	1543	638222450	638221861	0.000000e+00	719.0
16	TraesCS5B01G508500	chr4A	93.750	432	26	1	3458	3889	638220044	638219614	0.000000e+00	647.0
17	TraesCS5B01G508500	chr4A	82.550	149	13	6	3510	3645	395039389	395039537	6.850000e-23	119.0
18	TraesCS5B01G508500	chr6B	79.545	528	77	21	3372	3876	392492463	392491944	8.020000e-92	348.0
19	TraesCS5B01G508500	chr4D	79.480	346	38	15	3470	3796	215447003	215446672	8.490000e-52	215.0
20	TraesCS5B01G508500	chr2D	80.612	196	22	8	3697	3889	33723871	33724053	1.890000e-28	137.0
21	TraesCS5B01G508500	chr2D	86.667	105	14	0	436	540	562580333	562580437	2.460000e-22	117.0
22	TraesCS5B01G508500	chr7D	80.982	163	22	7	3199	3353	125879369	125879208	1.900000e-23	121.0
23	TraesCS5B01G508500	chr7D	80.982	163	22	7	3199	3353	125886276	125886115	1.900000e-23	121.0
24	TraesCS5B01G508500	chr7D	94.737	38	2	0	2544	2581	32644811	32644848	4.210000e-05	60.2
25	TraesCS5B01G508500	chr2B	100.000	28	0	0	423	450	52720464	52720491	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	TraesCS5B01G508500	chr5B	673678922	673682823	3901	False	3331.000000	5465	100.000000	1	3902	2	chr5B.!!$F4	3901
1	TraesCS5B01G508500	chr5B	673636177	673638791	2614	False	266.500000	429	83.700500	944	1921	2	chr5B.!!$F2	977
2	TraesCS5B01G508500	chr5B	673670126	673671608	1482	False	204.666667	335	88.891667	944	1517	3	chr5B.!!$F3	573
3	TraesCS5B01G508500	chr5D	533629834	533633426	3592	False	898.425000	2736	91.593750	535	3779	4	chr5D.!!$F3	3244
4	TraesCS5B01G508500	chr4A	638219614	638222450	2836	True	1073.000000	1853	89.581000	947	3889	3	chr4A.!!$R1	2942
5	TraesCS5B01G508500	chr6B	392491944	392492463	519	True	348.000000	348	79.545000	3372	3876	1	chr6B.!!$R1	504

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
520	521	0.028505	CGAGCCGCATGAATTCAAGG	59.971	55.0	13.09	16.32	0.00	3.61	F
1234	1787	0.175760	ATACGCATGCACGTCCTTCT	59.824	50.0	19.57	0.00	44.43	2.85	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2219	5534	0.179145	CCTTATTGTGCTGCTGCTGC	60.179	55.0	22.51	22.51	40.48	5.25	R
3196	6536	0.031994	AACCATTGCCGTGTTGAAGC	59.968	50.0	0.00	0.00	0.00	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
18	19	3.127099	ATCGGCTACTTCGATCCCA	57.873	52.632	0.00	0.00	42.82	4.37
19	20	1.633774	ATCGGCTACTTCGATCCCAT	58.366	50.000	0.00	0.00	42.82	4.00
20	21	0.959553	TCGGCTACTTCGATCCCATC	59.040	55.000	0.00	0.00	0.00	3.51
21	22	0.038159	CGGCTACTTCGATCCCATCC	60.038	60.000	0.00	0.00	0.00	3.51
22	23	1.048601	GGCTACTTCGATCCCATCCA	58.951	55.000	0.00	0.00	0.00	3.41
23	24	1.625818	GGCTACTTCGATCCCATCCAT	59.374	52.381	0.00	0.00	0.00	3.41
24	25	2.613977	GGCTACTTCGATCCCATCCATG	60.614	54.545	0.00	0.00	0.00	3.66
25	26	2.300152	GCTACTTCGATCCCATCCATGA	59.700	50.000	0.00	0.00	0.00	3.07
26	27	2.918712	ACTTCGATCCCATCCATGAC	57.081	50.000	0.00	0.00	0.00	3.06
27	28	2.118679	ACTTCGATCCCATCCATGACA	58.881	47.619	0.00	0.00	0.00	3.58
28	29	2.158900	ACTTCGATCCCATCCATGACAC	60.159	50.000	0.00	0.00	0.00	3.67
29	30	0.389025	TCGATCCCATCCATGACACG	59.611	55.000	0.00	0.00	0.00	4.49
30	31	0.389025	CGATCCCATCCATGACACGA	59.611	55.000	0.00	0.00	0.00	4.35
31	32	1.202521	CGATCCCATCCATGACACGAA	60.203	52.381	0.00	0.00	0.00	3.85
32	33	2.487934	GATCCCATCCATGACACGAAG	58.512	52.381	0.00	0.00	0.00	3.79
33	34	0.107703	TCCCATCCATGACACGAAGC	60.108	55.000	0.00	0.00	0.00	3.86
34	35	1.431488	CCCATCCATGACACGAAGCG	61.431	60.000	0.00	0.00	0.00	4.68
35	36	0.460109	CCATCCATGACACGAAGCGA	60.460	55.000	0.00	0.00	0.00	4.93
36	37	1.575244	CATCCATGACACGAAGCGAT	58.425	50.000	0.00	0.00	0.00	4.58
37	38	1.935873	CATCCATGACACGAAGCGATT	59.064	47.619	0.00	0.00	0.00	3.34
38	39	1.640428	TCCATGACACGAAGCGATTC	58.360	50.000	2.61	2.61	0.00	2.52
39	40	1.067213	TCCATGACACGAAGCGATTCA	60.067	47.619	14.56	0.00	0.00	2.57
40	41	1.325640	CCATGACACGAAGCGATTCAG	59.674	52.381	14.56	7.73	0.00	3.02
41	42	1.995484	CATGACACGAAGCGATTCAGT	59.005	47.619	14.56	11.06	0.00	3.41
42	43	2.148916	TGACACGAAGCGATTCAGTT	57.851	45.000	14.56	0.00	0.00	3.16

Showing 1 to 25 of 498 entries

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Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability
1	2	0.959553	GATGGGATCGAAGTAGCCGA	59.040	55.000	40.53	5.54
3	4	1.048601	TGGATGGGATCGAAGTAGCC	58.951	55.000	0.00	3.93
4	5	2.300152	TCATGGATGGGATCGAAGTAGC	59.700	50.000	0.00	3.58
5	6	3.321968	TGTCATGGATGGGATCGAAGTAG	59.678	47.826	0.00	2.57
6	7	3.069586	GTGTCATGGATGGGATCGAAGTA	59.930	47.826	0.00	2.24
8	9	2.487934	GTGTCATGGATGGGATCGAAG	58.512	52.381	0.00	3.79
9	10	1.202521	CGTGTCATGGATGGGATCGAA	60.203	52.381	0.00	3.71
11	12	0.389025	TCGTGTCATGGATGGGATCG	59.611	55.000	0.00	3.69
12	13	2.487934	CTTCGTGTCATGGATGGGATC	58.512	52.381	0.00	3.36
13	14	1.475751	GCTTCGTGTCATGGATGGGAT	60.476	52.381	0.00	3.85
14	15	0.107703	GCTTCGTGTCATGGATGGGA	60.108	55.000	0.00	4.37
16	17	0.460109	TCGCTTCGTGTCATGGATGG	60.460	55.000	0.00	3.51
17	18	1.575244	ATCGCTTCGTGTCATGGATG	58.425	50.000	0.00	3.51
18	19	2.205074	GAATCGCTTCGTGTCATGGAT	58.795	47.619	0.00	3.41
19	20	1.067213	TGAATCGCTTCGTGTCATGGA	60.067	47.619	33.86	3.41
20	21	1.325640	CTGAATCGCTTCGTGTCATGG	59.674	52.381	33.86	3.66
21	22	1.995484	ACTGAATCGCTTCGTGTCATG	59.005	47.619	33.86	3.07
22	23	2.370281	ACTGAATCGCTTCGTGTCAT	57.630	45.000	33.86	3.06
23	24	2.148916	AACTGAATCGCTTCGTGTCA	57.851	45.000	33.86	3.58
24	25	2.028165	GCTAACTGAATCGCTTCGTGTC	59.972	50.000	33.86	3.67
25	26	1.993370	GCTAACTGAATCGCTTCGTGT	59.007	47.619	33.86	4.49
26	27	1.992667	TGCTAACTGAATCGCTTCGTG	59.007	47.619	33.86	4.35
27	28	1.993370	GTGCTAACTGAATCGCTTCGT	59.007	47.619	33.86	3.85
28	29	1.324736	GGTGCTAACTGAATCGCTTCG	59.675	52.381	33.86	3.79
29	30	2.622436	AGGTGCTAACTGAATCGCTTC	58.378	47.619	0.00	3.86

Showing 1 to 25 of 509 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.