AutoCloner

Multiple sequence alignment - TraesCS2A01G422400

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	TraesCS2A01G422400	chr2A	100.000	3926	0	0	1	3926	677484602	677480677	0.000000e+00	7251
1	TraesCS2A01G422400	chr2A	87.826	345	36	6	1208	1548	677483057	677482715	2.200000e-107	399
2	TraesCS2A01G422400	chr2A	87.826	345	36	6	1546	1888	677483395	677483055	2.200000e-107	399
3	TraesCS2A01G422400	chr2D	90.026	3449	200	71	1	3365	533065238	533061850	0.000000e+00	4331
4	TraesCS2A01G422400	chr2D	86.994	346	37	7	1208	1548	533063649	533063307	2.210000e-102	383
5	TraesCS2A01G422400	chr2D	83.815	346	33	15	1546	1888	533063972	533063647	1.370000e-79	307
6	TraesCS2A01G422400	chr2D	92.019	213	15	1	3716	3926	533061134	533060922	8.250000e-77	298
7	TraesCS2A01G422400	chr2B	89.997	3429	208	68	1	3365	632626587	632623230	0.000000e+00	4307
8	TraesCS2A01G422400	chr2B	88.150	346	33	8	1208	1548	632625027	632624685	4.720000e-109	405
9	TraesCS2A01G422400	chr2B	81.792	346	31	12	1546	1888	632625341	632625025	1.080000e-65	261
10	TraesCS2A01G422400	chr7D	82.386	352	48	8	1875	2222	625200336	625200677	1.070000e-75	294
11	TraesCS2A01G422400	chr7A	80.299	335	55	3	1874	2207	436887189	436887513	3.920000e-60	243
12	TraesCS2A01G422400	chr3D	84.343	198	29	2	1875	2071	534211381	534211185	4.000000e-45	193
13	TraesCS2A01G422400	chr3B	82.828	198	32	2	1875	2071	706321683	706321487	4.030000e-40	176

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	TraesCS2A01G422400	chr2A	677480677	677484602	3925	True	2683.000000	7251	91.884000	1	3926	3	chr2A.!!$R1	3925
1	TraesCS2A01G422400	chr2D	533060922	533065238	4316	True	1329.750000	4331	88.213500	1	3926	4	chr2D.!!$R1	3925
2	TraesCS2A01G422400	chr2B	632623230	632626587	3357	True	1657.666667	4307	86.646333	1	3365	3	chr2B.!!$R1	3364

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	Hairpin	End Stability	Orientation
553	598	0.395724	CCCTTTGCTACCCCATCCAC	60.396	60.000	0.00	0.00	4.02	F
1281	1352	0.783206	TGGCTTGAGGGGAAATGGAA	59.217	50.000	0.00	0.00	3.53	F
2656	2735	1.518572	GTCGGCCGACGTGATGAAT	60.519	57.895	39.77	44.69	2.57	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
1861	1935	2.548493	GCAATCCTGCCACACACAAAAT	60.548	45.455	0.0	43.26	1.82	R
2844	2923	0.033504	ACACGAATTCCAGTGACGCT	59.966	50.000	17.2	40.56	5.07	R
3505	3611	1.127951	GATACAACCAAACGCCGTCTG	59.872	52.381	0.0	0.00	3.51	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
52	53	5.981315	CACCTAATGGAAAGCATTATTGCAG	59.019	40.000	11.88	0.00	43.33	4.41
119	140	2.124570	CCTCCCTTGCCATGTCCG	60.125	66.667	0.00	0.00	0.00	4.79
172	193	1.917336	TTTCCGGCCATCTGGTACCC	61.917	60.000	10.07	0.00	39.81	3.69
208	229	4.095410	TGAAACTCACACTTTGCACTTG	57.905	40.909	0.00	0.00	0.00	3.16
255	276	2.153645	TGCATTGTTTGAGATGCTCGT	58.846	42.857	9.39	0.00	46.68	4.18
296	317	1.182673	GCACACATTAGCGCGATTTG	58.817	50.000	12.10	8.01	0.00	2.32
314	335	1.485124	TGCGGATAGATGTCTGTGGT	58.515	50.000	0.00	0.00	0.00	4.16
316	337	1.409064	GCGGATAGATGTCTGTGGTCA	59.591	52.381	0.00	0.00	0.00	4.02
342	375	3.855689	AATAGTCTGTTTGTGCATGCC	57.144	42.857	16.68	7.25	0.00	4.40
346	379	2.063266	GTCTGTTTGTGCATGCCATTG	58.937	47.619	16.68	0.00	0.00	2.82
360	404	2.387757	GCCATTGGATTTAGGGCAGAA	58.612	47.619	6.95	0.00	44.01	3.02
392	436	4.757594	TGGCCACATTGCTTGATTTAATC	58.242	39.130	0.00	0.00	0.00	1.75
437	481	9.013490	CATGAAATGTTTATTTGCTGTACTAGC	57.987	33.333	9.52	9.52	45.83	3.42
504	548	5.067023	AGTCTTTGAGGCTTGAAACAAGAAG	59.933	40.000	14.44	8.86	0.00	2.85
543	587	3.346734	CCCCTGGCCCCTTTGCTA	61.347	66.667	0.00	0.00	0.00	3.49
548	593	3.668142	GGCCCCTTTGCTACCCCA	61.668	66.667	0.00	0.00	0.00	4.96
553	598	0.395724	CCCTTTGCTACCCCATCCAC	60.396	60.000	0.00	0.00	0.00	4.02
575	620	1.206072	CTGAAGAAGCACACGCAGC	59.794	57.895	0.00	0.00	42.27	5.25
577	622	2.203195	AAGAAGCACACGCAGCCA	60.203	55.556	0.00	0.00	42.27	4.75
578	623	2.449556	GAAGAAGCACACGCAGCCAC	62.450	60.000	0.00	0.00	42.27	5.01
579	624	3.279116	GAAGCACACGCAGCCACA	61.279	61.111	0.00	0.00	42.27	4.17
580	625	3.245948	GAAGCACACGCAGCCACAG	62.246	63.158	0.00	0.00	42.27	3.66
584	629	3.625897	ACACGCAGCCACAGCCTA	61.626	61.111	0.00	0.00	41.25	3.93
679	738	7.009723	GCTACTCTTTTACTCTTCACAGCATAC	59.990	40.741	0.00	0.00	0.00	2.39
792	851	2.550830	TGTGGAGCTTGGAAGAAGTC	57.449	50.000	0.00	0.00	0.00	3.01

Showing 1 to 25 of 258 entries

Previous1 2 3 4 5…11Next

Show entries

Search:

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
9	10	2.347490	CCCTTGGTCCACTCCACG	59.653	66.667	0.00	0.00	37.20	4.94
52	53	1.017387	CAAGGCAGGGAATAACTCGC	58.983	55.000	0.00	0.00	37.26	5.03
119	140	0.900421	ACTGGTAACCGCCTCTTACC	59.100	55.000	5.32	5.32	42.49	2.85
172	193	3.661944	AGTTTCAGTGTGCATGAGAGAG	58.338	45.455	0.00	0.00	0.00	3.20
208	229	7.096885	GCACAAGATTAATAATGCGTGTTGATC	60.097	37.037	0.00	0.00	0.00	2.92
255	276	4.792068	CCCTCAAATTAGCACCATTAGGA	58.208	43.478	0.00	0.00	38.69	2.94
296	317	1.409064	TGACCACAGACATCTATCCGC	59.591	52.381	0.00	0.00	0.00	5.54
314	335	7.503521	TGCACAAACAGACTATTATTGTTGA	57.496	32.000	0.00	0.00	35.39	3.18
316	337	6.808212	GCATGCACAAACAGACTATTATTGTT	59.192	34.615	14.21	0.00	36.66	2.83
342	375	5.665916	AACTTTCTGCCCTAAATCCAATG	57.334	39.130	0.00	0.00	0.00	2.82
346	379	6.835819	ACTTAAACTTTCTGCCCTAAATCC	57.164	37.500	0.00	0.00	0.00	3.01
360	404	3.387699	AGCAATGTGGCCAACTTAAACTT	59.612	39.130	7.24	0.00	0.00	2.66
392	436	6.182039	TCATGCAATAAGGAAAAGAGAACG	57.818	37.500	0.00	0.00	0.00	3.95
434	478	0.895530	GGCTGTCCCGCTATATGCTA	59.104	55.000	0.00	0.00	40.11	3.49
437	481	0.969149	TCAGGCTGTCCCGCTATATG	59.031	55.000	15.27	0.00	39.21	1.78
444	488	1.079543	CTCTTGTCAGGCTGTCCCG	60.080	63.158	15.27	2.90	39.21	5.14
543	587	0.995024	CTTCAGAAGGTGGATGGGGT	59.005	55.000	1.69	0.00	0.00	4.95
679	738	5.664457	TGTATGCATAGACAGGAGAAACTG	58.336	41.667	6.67	0.00	44.03	3.16
801	860	8.270744	AGAGTTCAGAAGCAAAGGTATTATCAT	58.729	33.333	0.00	0.00	0.00	2.45
802	861	7.624549	AGAGTTCAGAAGCAAAGGTATTATCA	58.375	34.615	0.00	0.00	0.00	2.15
803	862	8.394121	CAAGAGTTCAGAAGCAAAGGTATTATC	58.606	37.037	0.00	0.00	0.00	1.75
804	863	7.148171	GCAAGAGTTCAGAAGCAAAGGTATTAT	60.148	37.037	0.00	0.00	0.00	1.28
805	864	6.149474	GCAAGAGTTCAGAAGCAAAGGTATTA	59.851	38.462	0.00	0.00	0.00	0.98
806	865	5.048434	GCAAGAGTTCAGAAGCAAAGGTATT	60.048	40.000	0.00	0.00	0.00	1.89
835	894	7.554476	AGGAAGTAAGATAAAGCAGATGGTTTC	59.446	37.037	12.84	1.36	43.68	2.78

Showing 1 to 25 of 280 entries

Previous1 2 3 4 5…12Next

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.